Contacts of the helix formed by residues 139 - 160 (chain B) in PDB entry 2V62
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASP* 6.0 8.5 - - + +
138B PHE* 1.3 74.9 - - - +
140B LYS* 1.3 66.6 + - - +
141B SER* 4.5 7.4 - - - +
142B THR* 2.9 24.4 + - - +
143B VAL* 2.9 10.7 + - - +
324B ASP* 3.0 39.4 + - - +
325B PHE* 5.9 0.2 - - - -
326B SER* 4.2 20.2 - - - +
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE 3.5 2.0 + - - -
139B LYS* 1.3 71.3 - - - +
141B SER* 1.3 65.2 + - - +
142B THR 3.2 0.2 + - - -
143B VAL* 3.2 2.2 + - + +
144B LEU* 3.0 39.9 + - + +
244B LEU* 3.4 31.1 - - + +
282B GLY 5.7 0.7 - - - +
283B SER* 4.4 8.9 - - - -
284B SER* 2.8 54.7 + - - +
287B GLU* 2.9 30.4 + - - -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LYS* 4.5 6.6 - - - +
140B LYS* 1.3 78.4 - - - +
142B THR* 1.3 64.6 + - - +
144B LEU* 3.4 7.5 + - - +
145B GLN* 2.9 30.3 + - - +
324B ASP* 4.8 7.3 + - - +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 4.1 10.1 - - + -
139B LYS* 2.9 13.5 + - - +
141B SER* 1.3 75.1 + - - +
143B VAL* 1.3 61.3 + - - +
145B GLN* 3.8 6.0 - - - +
146B LEU* 2.8 47.7 + - + +
323B LEU* 4.4 8.3 - - + +
324B ASP* 2.7 50.8 + - - +
325B PHE* 4.0 23.1 - - + -
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.6 20.9 - - + +
139B LYS 2.9 17.2 + - - +
140B LYS* 3.2 9.2 + - - +
142B THR* 1.3 78.3 - - - +
144B LEU* 1.3 59.9 + - + +
146B LEU* 3.3 8.6 + - - +
147B GLY 3.1 23.0 + - - -
240B MET* 3.6 45.2 - - + +
243B TRP* 3.7 28.5 - - + -
244B LEU* 4.0 9.4 - - + +
288B ILE* 4.4 10.1 - - + -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 3.0 47.4 + - + +
141B SER* 3.9 6.3 - - - +
143B VAL* 1.3 78.0 - - + +
145B GLN* 1.3 64.7 + - - +
147B GLY* 3.4 2.0 + - - +
148B ILE* 3.2 29.1 + - + +
240B MET* 4.7 3.4 - - - -
244B LEU* 6.2 0.9 - - + -
287B GLU* 4.0 21.3 - - + +
288B ILE* 4.4 15.0 - - + -
313B LEU* 3.4 49.6 - - + +
315B PRO* 5.6 0.7 - - + -
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 2.9 19.5 + - - +
142B THR* 3.9 4.4 - - - +
144B LEU* 1.3 74.4 - - - +
146B LEU* 1.3 58.5 + - - +
148B ILE* 3.2 10.8 + - - +
149B ARG* 2.9 58.8 + - + +
320B LEU* 4.0 21.0 - - + +
321B GLY 3.0 37.8 + - - +
322B PRO 4.1 5.9 + - - -
323B LEU* 3.4 31.1 - - + +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 3.7 34.3 - - + -
138B PHE* 4.2 12.8 - - + -
142B THR* 2.8 43.2 + - + +
143B VAL* 3.6 4.7 - - - +
145B GLN* 1.3 72.8 - - - +
147B GLY* 1.3 57.4 + - - +
149B ARG* 3.8 3.8 - - - +
150B MET* 2.9 36.2 + - - +
172B LEU* 4.1 5.6 - - + -
182B VAL* 3.9 26.0 - - + -
243B TRP* 4.0 29.8 - - + -
323B LEU* 4.1 15.7 - - + -
325B PHE* 4.9 1.3 - - + -
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL 3.1 11.1 + - - -
144B LEU 3.4 1.3 + - - -
145B GLN 3.2 0.2 - - - -
146B LEU* 1.3 78.9 - - - +
148B ILE* 1.3 50.8 + - - +
150B MET 3.3 0.5 + - - -
151B LEU* 2.8 37.9 + - - +
236B LEU* 3.5 16.2 - - - +
240B MET* 3.8 25.1 - - - +
243B TRP* 5.0 0.2 - - - -
313B LEU* 3.7 7.6 - - - -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.2 20.5 + - + +
145B GLN* 3.2 6.8 + - - +
147B GLY* 1.3 73.5 - - - +
149B ARG* 1.3 64.7 + - - +
151B LEU* 3.3 10.1 + - - +
152B ASP* 3.1 26.6 + - - +
310B LYS* 4.0 31.6 - - + +
313B LEU* 3.7 20.8 - - + +
314B ASN* 3.9 28.5 - - + +
320B LEU* 4.0 36.6 - - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 5.8 1.4 - - - +
96B ASP* 2.7 43.4 + - - +
97B TYR* 3.2 38.1 + - + +
99B GLY 5.6 0.2 + - - -
145B GLN* 2.9 47.9 + - + +
146B LEU* 3.8 4.3 - - - +
148B ILE* 1.3 75.3 - - - +
150B MET* 1.3 65.2 + - + +
152B ASP* 3.3 20.9 + - - +
153B VAL* 3.3 23.6 + - - +
182B VAL* 3.8 22.4 - - + +
320B LEU* 3.6 31.3 + - - +
321B GLY 5.2 0.8 + - - -
323B LEU* 5.5 1.3 - - + -
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU 2.9 20.8 + - - +
147B GLY 3.7 3.8 - - - +
149B ARG* 1.3 82.9 - - + +
151B LEU* 1.3 59.5 + - - +
153B VAL* 3.2 9.7 + - + +
154B LEU* 2.8 36.9 + - + +
167B ILE* 4.6 9.0 - - + -
172B LEU* 4.0 27.1 - - + -
182B VAL* 4.0 26.2 - - + +
183B TYR 4.5 0.2 - - - -
184B LEU* 3.8 46.7 - - + +
236B LEU* 3.7 26.7 - - + -
243B TRP* 5.3 0.4 - - + -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY 2.8 24.3 + - - +
148B ILE* 3.3 5.6 + - - +
150B MET* 1.3 70.6 - - - +
152B ASP* 1.3 60.5 + - - +
154B LEU* 3.9 11.5 - - + +
155B GLU* 2.9 30.7 + - - +
233B VAL* 5.1 3.6 - - + -
236B LEU* 4.0 11.2 - - + +
291B PHE* 3.9 11.9 - - + -
306B TYR* 4.1 18.2 - - + +
309B LEU* 3.8 39.5 - - + -
310B LYS* 3.7 29.8 - - + -
313B LEU* 3.8 22.4 - - + -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 4.8 3.5 + - - -
95B LEU* 3.4 28.1 - - + +
97B TYR 5.0 3.3 - - - +
98B LEU* 3.7 21.8 - - + +
148B ILE* 3.1 20.0 + - - +
149B ARG* 3.5 26.3 + - - +
150B MET 3.3 0.2 - - - -
151B LEU* 1.3 76.7 - - - +
153B VAL* 1.3 61.3 + - - +
155B GLU* 3.5 9.0 + - - +
156B TYR* 3.3 16.5 + - - +
310B LYS* 2.7 33.3 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.0 8.5 - - + -
99B GLY* 3.6 39.3 - - - +
100B ILE* 3.8 18.8 - - + -
149B ARG 3.3 11.6 + - - +
150B MET* 3.2 19.1 + - + +
152B ASP* 1.3 76.2 - - - +
154B LEU* 1.3 58.9 + - - +
156B TYR* 3.2 3.9 + - - +
157B ILE* 3.0 36.3 + - + +
184B LEU* 3.8 26.9 - - + -
187B TYR* 4.0 4.0 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 2.8 21.1 + - + +
151B LEU* 3.9 10.3 - - + +
153B VAL* 1.3 73.0 - - - +
155B GLU* 1.3 67.4 + - - +
157B ILE* 3.3 15.2 + - + -
158B HIS* 2.8 44.2 + - + +
164B HIS* 4.8 0.4 - - + -
167B ILE* 3.9 21.1 - - + -
184B LEU* 4.6 8.7 - - + -
232B ASP* 3.6 53.2 - - + +
233B VAL* 4.3 6.5 - - + +
236B LEU* 4.2 17.0 - - + -
306B TYR* 4.4 4.0 - - + -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 4.0 24.6 - - + -
93B LYS* 5.4 4.9 - - - +
151B LEU 2.9 17.6 + - - +
152B ASP* 3.8 11.4 - - - +
154B LEU* 1.3 75.8 - - - +
156B TYR* 1.3 56.6 + - - +
158B HIS* 3.9 1.0 - - - +
159B GLU* 2.9 29.7 + - + +
303B LYS* 4.9 9.5 + - - -
306B TYR* 3.5 52.0 + - + +
310B LYS* 5.5 4.2 + - - +
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.6 29.1 + - + -
85B CYS* 3.5 27.0 - - - +
86B ILE* 3.5 23.8 - - + +
89B TRP* 3.5 57.1 - + + +
98B LEU* 3.7 13.7 - - + -
100B ILE* 3.4 19.3 - - + -
152B ASP 3.3 10.9 + - - +
153B VAL 3.2 8.6 + - - +
155B GLU* 1.3 78.7 - - - +
157B ILE* 1.3 61.6 + - - +
159B GLU* 3.3 2.7 + - - +
160B ASN* 2.9 52.5 + - - -
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 3.6 31.0 - - + -
80B VAL* 4.2 5.6 - - + -
100B ILE* 3.7 21.8 - - + -
153B VAL* 3.0 30.5 + - + +
154B LEU* 3.6 18.8 - - + +
156B TYR* 1.3 75.3 - - - +
158B HIS* 1.3 62.8 + - + +
160B ASN* 2.9 18.4 + - - +
161B GLU 3.1 0.3 + - - -
162B TYR* 3.0 29.3 + - + +
163B VAL 4.1 1.6 - - - -
164B HIS* 3.8 38.4 - - + +
184B LEU* 4.9 0.4 - - + -
187B TYR* 4.5 9.9 - - + -
232B ASP* 4.2 0.9 - - - +
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Residues in contact with HIS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 2.8 40.1 + - + +
155B GLU 4.0 0.9 - - - +
157B ILE* 1.3 76.9 - - + +
159B GLU* 1.3 64.5 + - - +
161B GLU* 3.0 9.2 + - - -
162B TYR 3.1 26.9 - - - -
163B VAL* 3.9 11.1 - - + +
193B TYR* 2.8 21.7 + - - -
229B ARG* 3.5 41.3 + - + +
232B ASP* 2.9 29.5 + - + +
233B VAL* 4.8 2.9 - - + -
304B PRO* 4.9 0.2 - - + -
306B TYR* 2.7 33.6 + + + +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 4.3 27.3 - - + -
155B GLU* 2.9 19.6 + - + +
156B TYR* 3.3 6.3 + - - +
158B HIS* 1.3 75.8 - - - +
160B ASN* 1.3 65.5 + - - +
161B GLU* 3.5 7.4 + - - +
303B LYS* 4.6 15.4 + - - -
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 4.8 6.7 - - - +
80B VAL* 3.7 24.3 - - + +
156B TYR* 2.9 55.8 + - - +
157B ILE 2.9 13.1 + - - +
159B GLU* 1.3 83.2 - - - +
161B GLU* 1.3 70.7 + - - +
162B TYR* 3.4 13.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il