Contacts of the helix formed by residues 160 - 175 (chain B) in PDB entry 4DKE
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 ARG 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 6.4 3.4 - - - +
61B ASN* 2.2 46.1 + - - +
62B TYR 3.9 12.8 - - - +
63B LYS* 4.0 26.2 - - + +
159B VAL* 1.3 78.2 - - - +
161B PRO* 1.3 70.6 - - + +
162B LYS* 4.1 5.8 - - + +
163B ALA* 2.9 30.8 + - + +
164B LEU* 3.1 12.3 + - - +
55H TYR 5.2 1.8 + - - -
56H TYR* 5.7 1.6 - - - -
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Residues in contact with PRO 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B MET* 3.6 31.9 - - - +
58B PHE* 4.0 39.3 - - + -
62B TYR* 3.3 19.7 - - + +
63B LYS* 4.3 1.3 - - - -
64B ILE* 4.3 15.7 - - + +
105B VAL* 4.1 21.3 - - + +
159B VAL* 3.7 6.0 - - - +
160B ARG* 1.3 84.2 - - + +
162B LYS* 1.3 58.2 + - - +
164B LEU* 3.7 7.5 + - + +
165B LEU* 3.5 14.9 + - - +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 4.3 26.7 + - - -
50B ARG* 4.2 15.0 - - + +
51B LEU* 4.4 18.4 - - + +
54B MET* 3.4 26.5 + - + +
55B LYS* 4.3 20.6 - - + +
160B ARG* 3.0 7.6 - - + +
161B PRO* 1.3 75.6 - - - +
163B ALA* 1.3 60.3 + - - +
164B LEU 3.0 1.7 + - - -
165B LEU* 3.3 1.4 + - - +
166B ASP* 2.8 67.2 + - - +
170B ARG* 5.2 4.0 - - - +
64H LYS* 6.0 2.4 - - - +
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 4.1 15.9 - - + -
160B ARG* 2.9 21.9 + - + +
162B LYS* 1.3 79.0 - - - +
164B LEU* 1.3 59.1 + - - +
166B ASP* 3.6 9.9 - - - +
167B ASN* 2.9 38.4 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.1 10.3 - - + -
66B VAL* 4.4 10.8 - - + -
70B GLY 3.7 24.5 - - - +
71B VAL* 5.3 0.9 - - - -
97B VAL* 6.0 0.2 - - + -
101B ALA* 4.1 28.8 - - + +
105B VAL* 3.8 26.2 - - + -
159B VAL* 3.7 36.6 - - + -
160B ARG 3.1 7.7 + - - +
161B PRO* 3.7 9.2 - - + +
162B LYS 3.0 0.8 - - - -
163B ALA* 1.3 77.1 - - - +
165B LEU* 1.3 65.5 + - + +
167B ASN* 3.1 23.0 + - - +
168B CYS* 3.1 11.4 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.9 18.7 - - + +
50B ARG* 4.1 16.2 - - + -
54B MET* 3.2 42.4 - - + -
98B SER* 5.7 0.4 - - - +
101B ALA* 5.0 8.3 - - + -
102B THR* 4.6 21.3 - - + +
105B VAL* 6.0 1.8 - - + -
118B TYR* 3.9 23.6 - - + +
119B LEU* 4.7 7.2 - - + -
122B VAL* 5.0 3.6 - - + -
161B PRO 3.5 2.8 + - - +
162B LYS 3.3 5.0 + - - +
164B LEU* 1.3 80.3 - - + +
166B ASP* 1.3 68.8 + - - +
168B CYS* 3.0 13.1 + - + +
169B PHE* 2.8 23.4 + - - +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ARG* 2.8 34.5 + - - +
162B LYS* 2.8 64.1 + - - +
163B ALA* 3.6 10.0 - - - +
165B LEU* 1.3 69.3 - - - +
167B ASN* 1.3 57.1 + - - +
169B PHE* 3.0 4.3 + - - +
170B ARG* 2.8 63.1 + - - +
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLY 5.2 0.2 + - - -
71B VAL* 4.3 10.9 - - - +
72B PHE* 3.3 28.5 - - + +
73B ARG* 3.2 37.0 - - - +
97B VAL* 6.5 0.2 - - + -
159B VAL* 5.5 2.2 - - - +
163B ALA* 2.9 28.3 + - - +
164B LEU* 3.1 15.6 + - + +
166B ASP* 1.3 77.9 - - - +
168B CYS* 1.3 61.8 + - - +
170B ARG* 4.8 9.1 + - - +
171B VAL* 3.0 32.1 + - - +
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 5.6 0.4 - - - -
45B LEU* 4.0 20.2 - - + -
94B TRP* 2.8 40.2 + - - +
98B SER* 2.9 36.3 - - - +
101B ALA* 6.3 1.1 - - + -
122B VAL* 6.1 0.4 - - - -
126B LEU* 4.5 9.0 - - - -
164B LEU 3.1 8.4 + - - +
165B LEU* 3.0 20.2 + - + +
167B ASN* 1.3 76.9 - - - +
169B PHE* 1.3 63.0 + - - +
172B MET* 3.0 11.3 + - - +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 4.1 31.2 - - + -
45B LEU* 3.3 37.4 - - + +
46B GLN* 4.6 4.3 - - - -
47B TYR 5.5 1.1 - - - -
50B ARG* 3.3 26.7 - - - +
165B LEU 2.8 13.1 + - - +
166B ASP 3.4 7.2 - - - +
168B CYS* 1.3 74.1 - - - +
170B ARG* 1.3 75.8 + - + +
172B MET* 3.2 18.6 + - + +
173B GLU* 3.2 54.1 + - + +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 6.3 0.8 - - - -
50B ARG* 5.1 8.6 - - - +
73B ARG* 6.0 3.2 - - - +
74B ILE* 4.9 16.2 - - + +
162B LYS* 5.2 3.4 - - - +
166B ASP* 2.8 51.6 + - - +
167B ASN* 4.2 7.9 + - - +
169B PHE* 1.3 85.0 - - + +
171B VAL* 1.3 65.2 + - + +
173B GLU* 3.1 17.2 + - - +
174B LEU* 3.2 12.8 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.3 36.6 - - + +
73B ARG* 3.7 23.1 - - - +
74B ILE* 3.9 5.8 - - + +
77B VAL* 4.9 7.6 - - + -
94B TRP* 3.5 21.1 - - + -
167B ASN* 3.0 19.6 + - - +
170B ARG* 1.3 72.4 - - + +
172B MET* 1.3 68.7 + - - +
173B GLU 3.1 0.9 + - - -
174B LEU* 3.1 7.4 + - + +
175B LEU* 3.1 40.8 + - + +
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Residues in contact with MET 172 (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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38B THR* 3.9 17.3 - - - +
41B LEU* 3.9 19.7 - - + -
42B ARG* 3.9 35.9 - - + +
45B LEU* 5.0 4.3 - - + -
94B TRP* 3.3 36.4 - - + +
168B CYS 3.0 20.1 + - - +
169B PHE* 3.2 25.3 + - + +
171B VAL* 1.3 76.5 - - - +
173B GLU* 1.3 65.9 + - + +
175B LEU* 4.9 1.1 - - - -
176B TYR* 3.0 45.9 + - + +
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Residues in contact with GLU 173 (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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42B ARG* 3.0 44.5 + - - +
169B PHE* 3.2 38.4 + - + +
170B ARG* 3.1 11.0 + - - +
171B VAL 3.1 0.8 - - - -
172B MET* 1.3 78.5 - - + +
174B LEU* 1.3 56.2 + - - +
175B LEU 3.0 4.5 - - - -
176B TYR* 2.8 22.0 + - - +
177B CYS* 2.9 28.0 + - + +
178B SER 4.3 0.9 + - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.2 18.8 - - + -
77B VAL* 3.2 39.0 - - + -
78B THR* 5.4 3.4 - - - +
81B GLN* 4.8 13.1 + - - +
87B GLU* 4.9 3.3 - - - +
170B ARG 3.2 8.4 + - - +
171B VAL* 3.1 11.7 + - - +
173B GLU* 1.3 77.7 - - - +
175B LEU* 1.3 64.4 + - + +
178B SER* 4.8 11.0 - - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.7 27.6 - - + -
81B GLN* 4.9 5.2 - - - +
87B GLU* 4.7 17.6 - - - +
90B LEU* 3.6 38.6 - - + +
91B ARG* 3.2 41.2 + - + -
94B TRP* 4.1 10.8 - - + -
171B VAL* 3.1 32.6 + - + +
172B MET* 3.9 3.8 - - - +
173B GLU 3.0 0.8 - - - -
174B LEU* 1.3 87.1 - - + +
176B TYR* 1.3 66.5 + - + +
178B SER* 5.3 1.8 - - - -
179B CYS* 4.6 3.1 - - - +
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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