Contacts of the helix formed by residues 140 - 159 (chain D) in PDB entry 4NY0
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 ASP 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D LYS 3.9 1.9 - - - +
77D VAL* 3.9 2.1 - - - -
78D LYS* 2.9 38.8 + - + +
79D HIS* 2.9 40.5 + - + +
136D GLN 4.4 0.4 - - - +
137D PHE 2.9 13.3 + - - +
139D GLU* 1.3 82.1 - - - +
141D LYS* 1.3 59.1 + - - +
142D PRO* 3.7 11.9 - - - +
143D THR* 2.9 42.4 + - - -
144D LEU 3.3 3.1 + - - -
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D PHE 4.0 4.3 - - - -
138D THR* 3.2 20.9 + - - +
139D GLU 5.3 0.4 - - - -
140D ASP* 1.3 68.5 - - - +
142D PRO* 1.3 72.8 - - + +
144D LEU* 3.7 10.5 - - + +
145D ASN* 2.8 40.1 + - - +
237D GLU* 2.6 36.4 + - + +
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Residues in contact with PRO 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 4.0 13.4 - - + -
75D HIS* 3.3 29.4 - - + +
76D LYS* 4.0 11.9 - - + +
77D VAL* 4.2 13.7 - - + -
140D ASP* 3.3 10.5 - - - +
141D LYS* 1.3 92.5 - - + +
143D THR* 1.3 55.6 + - - +
145D ASN* 3.7 6.3 - - + +
146D PHE* 2.8 27.5 + - - +
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 3.5 10.7 - - - +
79D HIS* 4.4 2.7 + - + +
82D CYS* 5.6 0.2 - - + -
83D TYR* 2.9 23.6 + - + +
126D ILE* 3.5 23.8 - - + -
137D PHE* 3.6 32.8 - - + -
140D ASP* 2.9 30.6 + - - -
142D PRO* 1.3 75.7 - - - +
144D LEU* 1.3 59.3 + - - +
146D PHE* 4.1 0.2 - - - -
147D PHE* 2.6 34.1 + - - +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D LEU* 4.5 10.5 - - + +
137D PHE* 3.6 36.2 + - + +
138D THR* 4.1 25.4 - - + -
140D ASP 3.3 3.8 + - - -
141D LYS* 3.8 14.4 - - + +
143D THR* 1.3 77.1 - - - +
145D ASN* 1.3 58.6 + - - +
147D PHE* 3.5 1.7 + - + +
148D TYR* 2.9 28.8 + - - +
237D GLU* 4.6 17.7 - - + +
240D ILE* 3.9 34.3 - - + -
241D LEU* 4.6 7.0 - - + -
244D PHE* 4.1 12.6 - - + -
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR 4.8 0.7 - - - -
44D GLU* 5.0 8.0 - - + +
141D LYS* 2.8 34.5 + - - +
142D PRO* 3.7 6.2 - - + +
144D LEU* 1.3 77.1 - - - +
146D PHE* 1.3 64.6 + - - +
148D TYR* 3.3 7.5 + - - +
149D GLN* 3.0 31.4 + - + +
178D ARG* 4.1 16.1 + - - -
240D ILE* 3.6 19.7 - - - +
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D HIS* 4.0 4.5 - - + -
42D TYR* 3.4 44.8 + + + +
43D PHE* 3.5 40.4 - + + -
83D TYR* 3.9 18.6 - + - +
124D LEU* 3.2 33.4 - - + -
126D ILE* 3.5 24.5 - - + -
142D PRO 2.8 22.2 + - - +
143D THR 3.0 3.8 + - - +
145D ASN* 1.3 73.3 - - - +
147D PHE* 1.3 61.8 + - - +
149D GLN* 3.3 2.6 + - - +
150D GLN* 3.0 41.9 + - - -
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Residues in contact with PHE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 3.7 30.7 - - + -
129D LEU* 4.1 27.8 - - + -
133D PHE* 4.0 22.4 - + - -
134D LEU* 4.4 2.7 - - + -
137D PHE* 4.0 20.9 - + + -
143D THR 2.6 20.1 + - - +
144D LEU* 3.8 3.1 - - + +
146D PHE* 1.3 74.8 - - - +
148D TYR* 1.3 56.0 + - - +
150D GLN* 3.2 16.1 + - - +
151D VAL* 2.8 52.8 + - + +
244D PHE* 3.7 30.1 - + - -
253D PHE* 3.9 19.3 - + - -
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Residues in contact with TYR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU 2.9 18.6 + - - +
145D ASN* 3.5 4.5 - - - +
147D PHE* 1.3 74.6 - - - +
149D GLN* 1.3 69.9 + - + +
151D VAL* 3.1 1.9 + - - +
152D LYS* 2.8 55.6 + - + +
174D LEU 4.7 0.9 - - - -
175D GLU* 2.9 32.3 + - - +
178D ARG* 3.4 33.6 - - - -
240D ILE* 3.8 36.6 - - + -
243D PHE* 3.5 46.5 - + + -
244D PHE* 3.7 12.9 - + - -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.7 30.7 - - + +
44D GLU* 4.1 15.2 + - + -
49D PRO* 5.8 0.3 - - - +
52D TRP* 3.6 24.2 - - + -
145D ASN* 3.0 19.1 + - + +
146D PHE 3.6 6.7 - - - +
148D TYR* 1.3 84.6 - - + +
150D GLN* 1.3 57.9 + - - +
152D LYS* 3.1 30.9 + - - +
153D SER* 2.8 32.9 + - - -
178D ARG* 3.5 32.7 - - - +
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Residues in contact with GLN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.5 21.6 - - + -
125D ARG* 3.4 44.0 - - - +
126D ILE* 2.7 48.7 + - - -
146D PHE* 3.0 19.6 + - + +
147D PHE* 3.5 23.8 - - - +
149D GLN* 1.3 78.4 - - - +
151D VAL* 1.3 62.2 + - - +
153D SER* 3.8 1.4 - - - -
154D ASP* 3.2 25.3 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE* 2.8 52.8 + - + +
148D TYR 3.8 2.2 - - - +
150D GLN* 1.3 78.6 - - + +
152D LYS* 1.3 59.9 - - - +
154D ASP* 3.4 7.8 + - - +
155D TYR* 3.0 27.2 + - - +
243D PHE* 5.0 1.1 - - + -
244D PHE* 3.9 17.3 - - + -
247D LEU* 3.7 26.2 - - + -
251D TYR* 4.8 3.5 - - + -
253D PHE* 3.9 27.4 - - + -
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PRO* 5.7 7.1 - - - +
52D TRP* 5.6 2.2 - - - -
148D TYR* 2.8 46.4 + - + +
149D GLN* 3.1 35.7 + - - +
151D VAL* 1.3 73.8 - - - +
153D SER* 1.3 61.9 + - - +
155D TYR* 3.2 10.2 + - + +
156D MET* 3.1 33.2 + - + +
175D GLU* 3.5 31.5 + - + +
205D ARG 5.1 6.4 + - - +
243D PHE* 4.1 22.8 - - + -
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Residues in contact with SER 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.6 30.0 + - - -
149D GLN 2.8 20.3 + - - -
150D GLN 3.8 1.3 - - - -
152D LYS* 1.3 74.1 - - - +
154D ASP* 1.3 65.2 + - - +
156D MET* 3.4 3.9 + - - +
157D LEU* 2.9 48.1 + - - +
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 4.3 4.3 + - - -
86D ARG* 5.6 0.7 + - - -
125D ARG* 2.7 40.4 + - - -
150D GLN* 3.2 17.7 + - - +
151D VAL* 3.7 8.2 - - - +
152D LYS 3.3 0.2 - - - -
153D SER* 1.3 77.8 + - - +
155D TYR* 1.3 61.5 + - - +
157D LEU* 4.7 5.7 - - - +
158D GLU* 3.1 38.1 + - - +
251D TYR* 3.3 23.4 + - + +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D VAL 3.0 14.4 + - - +
152D LYS* 3.2 14.6 - - + +
153D SER 3.1 0.2 - - - -
154D ASP* 1.3 76.6 - - - +
156D MET* 1.3 81.8 + - + +
159D ILE* 2.9 32.5 + - + -
160D ALA* 2.8 51.0 + - + +
163D VAL* 3.8 13.3 - - + +
168D ALA* 3.5 29.5 + - - +
171D LEU* 3.4 31.3 - - + +
206D PHE 5.6 2.7 - - - -
208D PRO* 5.0 2.1 - - + +
243D PHE* 4.5 11.0 - + - -
247D LEU* 3.8 28.5 - - + -
251D TYR* 4.7 4.5 - - + -
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Residues in contact with MET 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D LYS* 3.1 22.1 + - + +
153D SER* 3.8 7.2 - - - +
155D TYR* 1.3 97.7 - - + +
157D LEU* 1.3 70.8 + - + +
158D GLU 3.2 1.9 + - - -
160D ALA* 3.6 19.5 + - - +
161D ASP* 5.0 6.4 + - - +
204D LYS 3.7 23.6 - - - +
205D ARG* 4.3 8.1 - - - +
206D PHE 4.0 21.1 - - - +
207D PHE 3.9 16.8 - - - +
208D PRO* 4.5 2.5 - - + -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D THR* 6.2 4.7 - - + -
153D SER* 2.9 43.5 + - - +
154D ASP* 4.2 6.5 - - - +
156D MET* 1.3 83.4 - - + +
158D GLU* 1.3 62.4 + - + +
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASP* 3.1 21.1 + - - +
156D MET 3.2 1.9 + - - -
157D LEU* 1.3 86.2 - - + +
159D ILE* 1.3 69.6 + - + +
160D ALA 3.9 0.7 - - - -
161D ASP 5.6 0.2 - - - -
162D GLN* 3.8 17.8 + - - +
251D TYR* 3.0 31.0 + - + +
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Residues in contact with ILE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D TYR* 2.9 34.1 + - + +
158D GLU* 1.3 84.8 - - + +
160D ALA* 1.3 68.6 + - - +
161D ASP 3.3 2.9 - - - -
162D GLN* 3.2 27.9 + - + +
163D VAL* 3.3 20.1 + - + +
247D LEU* 4.4 2.7 - - + -
250D VAL* 4.3 13.2 - - + +
251D TYR* 3.6 51.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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