Contacts of the helix formed by residues 135 - 154 (chain B) in PDB entry 1P7L
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 PRO 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B TYR* 4.0 25.4 - - + -
127B THR* 3.3 9.6 - - + -
129B GLU* 3.5 5.6 - - - +
134B MET* 1.3 106.9 - - + +
136B ALA* 1.3 62.1 + - - +
137B PRO* 4.4 3.4 - - + -
138B ILE* 3.5 9.9 - - + +
139B THR* 3.0 22.5 - - - +
251B TYR* 4.0 21.1 - - + +
254B MET* 4.1 28.3 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLU* 2.5 27.0 + - + +
130B THR* 4.2 12.3 - - + +
134B MET 3.6 0.6 + - - -
135B PRO* 1.3 69.9 - - - +
137B PRO* 1.3 71.1 - - + +
139B THR* 2.3 30.0 + - - +
140B TYR* 3.1 24.7 + - + -
170B PHE* 4.3 8.7 - - + -
172B TYR* 4.4 1.3 - - - +
177B ILE* 4.5 8.7 - - + -
215B TRP* 5.2 2.2 - - + -
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Residues in contact with PRO 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.9 23.6 - - + -
7B SER* 3.6 26.1 - - - +
129B GLU* 3.7 0.4 - - - +
135B PRO* 3.8 3.1 - - + -
136B ALA* 1.3 93.8 - - + +
138B ILE* 1.3 62.8 + - - +
140B TYR* 3.5 1.7 + - - +
141B ALA* 3.2 23.6 + - - +
168B VAL* 5.0 2.4 - - - +
170B PHE* 3.3 36.4 - - + -
172B TYR* 3.4 21.8 - - + +
254B MET* 4.3 5.2 - - + -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 4.0 4.6 - - - -
8B GLU 3.7 24.5 - - - +
9B SER* 4.7 0.2 - - - +
134B MET* 3.9 23.6 - - + -
135B PRO* 3.5 18.3 - - + +
137B PRO* 1.3 78.5 - - - +
139B THR* 1.3 68.5 + - + +
141B ALA* 4.5 0.9 - - - -
142B HIS* 3.1 51.0 + - + +
248B VAL* 3.8 12.6 - - - +
250B THR 4.5 4.7 - - - +
251B TYR 3.9 19.9 + - - +
252B GLY* 3.8 22.9 - - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 4.8 8.8 - - + +
132B VAL* 4.8 6.3 - - + -
134B MET* 3.7 24.0 - - + +
135B PRO 3.0 20.2 - - - +
136B ALA* 2.3 34.5 + - - -
138B ILE* 1.3 85.7 - - + +
140B TYR* 1.3 67.5 + - - -
142B HIS* 3.5 7.3 + - - +
143B ARG* 2.8 43.1 + - - +
361B GLY* 6.2 0.9 - - - -
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR* 5.9 2.9 - - + +
136B ALA* 3.1 21.0 + - + +
137B PRO 4.2 0.9 - - - +
139B THR* 1.3 87.6 + - - +
141B ALA* 1.3 59.6 + - - +
143B ARG* 3.2 39.5 + - - +
144B LEU* 2.9 33.0 + - - +
168B VAL* 5.2 2.2 - - + -
170B PHE* 3.4 33.0 - + + -
210B ILE* 4.1 15.8 - - + +
211B LEU* 4.4 13.5 - - + -
212B PRO* 4.0 18.3 - - + +
215B TRP* 3.2 35.7 - + - -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER 4.7 1.3 - - - +
8B GLU* 3.9 13.7 - - - +
9B SER* 3.5 21.4 - - - +
137B PRO 3.2 17.9 + - - +
138B ILE* 4.0 4.7 - - - +
140B TYR* 1.3 76.0 - - - +
142B HIS* 1.3 63.9 + - - +
144B LEU* 3.1 15.0 + - - -
145B VAL 3.2 5.7 + - - -
166B SER* 2.9 29.5 + - - +
168B VAL* 4.5 10.0 - - + +
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Residues in contact with HIS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 2.5 30.1 + - - -
134B MET* 6.1 1.8 - - + +
138B ILE* 3.1 38.7 + - + +
139B THR* 3.7 6.5 - - - +
141B ALA* 1.3 74.7 - - - +
143B ARG* 1.3 65.1 + - + +
145B VAL* 3.1 5.9 - - - +
146B GLN* 2.9 34.0 + - - +
248B VAL* 3.1 31.6 + - + -
250B THR 5.4 0.8 + - - -
357B TYR* 3.4 27.1 - - - +
358B GLY* 3.2 28.4 - - - -
360B PHE 5.3 4.9 - - - -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 6.4 0.6 - - - +
139B THR* 2.8 32.9 + - - +
140B TYR* 3.2 42.1 + - - +
142B HIS* 1.3 77.7 - - + +
144B LEU* 1.3 57.0 + - - +
146B GLN* 3.7 12.6 - - - +
147B ARG* 2.8 32.1 + - - +
210B ILE* 3.7 28.5 + - + +
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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 TYR 2.9 17.1 + - - +
141B ALA* 3.1 9.4 + - - +
143B ARG* 1.3 75.5 - - - +
145B VAL* 1.3 63.6 + - - +
147B ARG* 3.2 6.4 + - - +
148B GLN* 3.1 18.7 + - - +
166B SER* 3.9 16.2 - - - -
168B VAL* 3.4 32.8 - - + -
183B VAL* 5.4 4.3 - - + -
184B VAL 5.2 2.0 - - - +
185B LEU* 4.2 9.6 - - + -
206B ILE* 3.5 28.6 - - + +
207B ILE* 4.0 18.4 - - + -
210B ILE* 3.5 21.3 - - + -
211B LEU* 4.0 14.4 - - + -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 4.0 8.1 - - - +
10B VAL* 3.6 15.0 - - - +
11B SER* 3.5 29.0 - - - +
141B ALA 3.2 6.7 + - - +
142B HIS 3.1 15.7 - - - +
144B LEU* 1.3 78.4 - - - +
146B GLN* 1.3 61.7 + - - +
148B GLN* 3.4 10.8 + - - +
149B ALA* 3.1 23.2 + - - +
164B ALA* 4.1 5.6 - - + +
165B LYS* 4.1 4.3 - - - -
166B SER* 3.7 33.4 - - - +
185B LEU* 5.5 2.5 - - + -
357B TYR* 3.6 19.3 - - + -
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 2.9 27.5 + - - +
143B ARG* 3.7 11.2 - - - +
145B VAL* 1.3 80.0 - - - +
147B ARG* 1.3 61.0 + - - +
149B ALA* 3.5 3.3 + - - +
150B GLU* 3.2 21.7 + - - +
357B TYR* 3.6 46.1 + - + +
362B ARG* 5.9 2.7 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ARG 2.8 18.8 + - - +
144B LEU 3.5 4.9 - - - +
146B GLN* 1.3 74.5 - - - +
148B GLN* 1.3 66.9 + - - +
150B GLU* 2.8 34.3 + - - +
151B VAL* 2.8 24.2 + - + +
154B ASN* 6.0 2.5 - - - +
156B THR* 5.7 1.0 + - - +
205B GLU* 2.6 47.2 + - - +
206B ILE* 3.6 22.9 - - + +
209B PRO* 4.2 15.8 - - - +
210B ILE* 3.8 20.4 - - + -
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 4.0 4.7 - - - -
144B LEU 3.1 9.3 + - - +
145B VAL* 3.6 14.0 - - - +
147B ARG* 1.3 78.2 - - - +
149B ALA* 1.3 78.3 + - - +
151B VAL* 2.9 25.3 - - - +
152B ARG* 3.1 20.8 + - - +
160B LEU* 3.5 11.9 - - + +
161B ARG 3.0 27.1 + - - -
162B PRO 4.0 0.2 + - - -
164B ALA* 3.6 23.2 - - + +
185B LEU* 5.3 4.3 - - + -
187B THR* 3.2 21.5 + - - +
206B ILE* 3.5 26.2 - - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 5.4 0.7 - - - -
12B GLU* 3.6 12.1 - - + +
145B VAL 3.1 9.6 + - - +
146B GLN 3.6 5.4 - - - +
147B ARG 3.1 0.8 - - - -
148B GLN* 1.3 88.5 + - - +
150B GLU* 1.3 58.4 + - - +
152B ARG* 3.4 17.9 + - - +
153B LYS* 3.0 36.0 + - + +
357B TYR* 3.4 25.8 - - + +
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Residues in contact with GLU 150 (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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146B GLN 3.2 10.5 + - - +
147B ARG* 2.8 29.4 + - - +
149B ALA* 1.3 76.8 - - - +
151B VAL* 1.3 58.3 + - - +
152B ARG 3.0 5.2 - - - -
153B LYS* 4.1 6.9 - - - +
154B ASN* 2.9 46.3 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG* 2.8 28.3 + - - +
148B GLN* 2.9 32.8 - - - +
150B GLU* 1.3 78.6 - - - +
152B ARG* 1.3 57.1 + - - +
154B ASN* 2.8 21.5 - - - +
156B THR* 3.1 26.5 + - + +
157B LEU* 2.9 37.4 + - + -
160B LEU* 3.6 11.7 - - + -
205B GLU* 3.7 8.5 - - + -
206B ILE* 4.1 10.8 - - + -
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Residues in contact with ARG 152 (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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11B SER* 5.2 0.2 + - - -
12B GLU* 4.6 7.7 - - - +
75B ILE 2.8 29.3 + - - -
76B GLY* 4.5 3.2 - - - -
148B GLN* 3.1 38.3 + - - +
149B ALA* 3.4 18.7 + - - +
150B GLU 3.0 0.2 - - - -
151B VAL* 1.3 78.2 - - - +
153B LYS* 1.3 88.2 + - - +
155B GLY* 3.2 12.8 + - - -
157B LEU 4.0 10.2 - - - +
158B PRO* 4.9 4.2 - - - +
160B LEU* 3.4 37.2 - - + +
161B ARG 3.5 15.7 - - - -
162B PRO* 3.4 29.8 + - - +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 2.6 39.8 + - - -
74B GLU 3.9 17.2 + - - +
149B ALA* 3.0 27.6 + - + +
150B GLU* 4.1 5.4 - - - +
152B ARG* 1.3 89.9 - - - +
154B ASN* 1.3 59.7 + - - +
155B GLY* 3.0 6.3 + - - -
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Residues in contact with ASN 154 (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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147B ARG* 6.0 2.8 - - - +
150B GLU* 2.9 37.3 + - - +
151B VAL* 2.8 13.9 - - - +
153B LYS* 1.3 75.9 - - - +
155B GLY* 1.3 58.7 + - - +
156B THR* 2.6 47.6 + - - -
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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