Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 1CPJ
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 3.9 11.8 - - + +
74A GLY 3.4 11.0 - - - +
75A TYR* 1.3 84.2 - - + -
77A SER* 1.3 58.2 + - - +
79A ALA* 2.9 30.0 + - + +
80A TRP* 3.1 13.6 - - - -
171A GLU* 3.7 34.3 - - + +
172A GLY 5.2 3.1 - - - +
173A ALA* 5.4 7.2 - - + -
200A ALA* 4.5 9.6 - - + -
245A GLU* 5.5 7.4 - - + +
247A VAL* 4.3 14.6 - - + -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 4.6 0.3 - - - +
76A PRO* 1.3 78.8 - - - +
78A GLY* 1.3 60.0 + - - +
80A TRP* 3.5 2.4 + - - +
81A ASN* 3.0 28.0 + - - +
150A SER* 5.0 0.3 + - - -
152A SER* 5.0 4.7 - - - -
247A VAL* 4.1 26.5 - - - +
155B ASP* 3.5 23.9 + - - -
244B SER* 2.8 39.6 + - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 2.8 35.4 + - - -
67A CYS* 3.5 8.7 - - - -
75A TYR 2.7 16.0 + - - -
77A SER* 1.3 74.3 + - - +
79A ALA* 1.3 54.3 + - - -
81A ASN* 3.2 3.8 + - - -
82A PHE* 2.8 28.9 + - - +
155B ASP* 5.2 1.1 - - - -
238B ASN* 4.1 7.1 + - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.2 7.9 - - + +
34A ALA* 3.8 24.9 - - + -
38A MET* 4.4 3.1 - - - -
59A LEU* 3.9 21.6 - - + +
67A CYS* 3.6 11.7 - - - -
75A TYR 3.3 3.8 + - - -
76A PRO* 2.9 22.6 + - + +
78A GLY* 1.3 76.9 - - - +
80A TRP* 1.3 56.0 + - - +
82A PHE* 3.1 3.5 + - - +
83A TRP* 3.0 25.8 + - - +
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Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 3.6 17.0 - - - +
37A ALA* 3.9 25.4 - - + -
38A MET* 3.5 27.6 - - + -
41A ARG* 4.2 10.5 - - - -
76A PRO 3.1 25.4 + - - -
77A SER 4.2 3.1 - - - +
79A ALA* 1.3 82.3 - - + +
81A ASN* 1.3 61.8 + - - +
83A TRP* 3.5 38.4 - + - +
84A THR* 3.1 28.6 + - - +
150A SER* 3.5 17.2 - - - +
169A PRO 5.1 0.2 - - - -
171A GLU* 2.8 27.5 + - + +
247A VAL* 3.5 33.7 - - + +
248A ALA* 3.5 18.6 - - + -
249A GLY* 3.4 18.8 - - - -
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Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 3.2 18.4 + - - +
77A SER 3.0 19.9 + - - +
78A GLY* 3.3 2.3 - - - +
80A TRP* 1.3 75.0 - - - +
82A PHE* 1.3 65.4 + - - +
84A THR* 2.7 25.5 + - - -
85A ARG* 3.2 28.2 + - - +
150A SER* 3.3 17.8 + - - -
155B ASP* 3.2 39.4 + - - +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP 4.8 1.1 - - - -
59A LEU* 3.8 18.6 - - + -
62A CYS* 3.7 24.5 - - + -
63A CYS* 3.6 40.8 - - + -
66A GLN* 2.9 15.3 - - - +
78A GLY 2.8 16.6 + - - +
79A ALA 3.5 3.6 - - - +
81A ASN* 1.3 73.5 - - - +
83A TRP* 1.3 59.4 + - - +
85A ARG* 3.1 4.9 + - - +
86A LYS* 2.7 64.2 + - + +
87A GLY 2.9 21.8 + - - -
88A LEU* 3.7 15.5 - - + -
140A TYR* 5.3 0.2 - - - -
144A LYS* 4.3 5.8 - - - -
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Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 3.7 38.9 - - + +
41A ARG* 5.4 0.2 - - + -
42A ILE* 4.5 9.6 - - + +
54A VAL* 5.4 0.8 - - - +
79A ALA 3.0 12.2 + - - +
80A TRP* 3.5 50.5 - + - +
81A ASN 3.2 0.2 - - - -
82A PHE* 1.3 78.1 - - - +
84A THR* 1.3 61.2 + - + +
87A GLY* 3.0 25.7 - - - -
88A LEU* 3.9 23.4 - - + +
145A HIS* 3.0 31.5 + - - +
146A TYR* 3.6 6.9 - - - -
147A GLY* 3.1 36.0 + - - +
149A THR 4.4 1.1 - - - -
249A GLY* 4.1 8.5 - - - -
250A ILE 3.8 8.1 - - - -
251A PRO* 3.8 37.0 - - + -
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TRP 3.1 13.2 + - - +
81A ASN* 2.7 23.5 + - - -
83A TRP* 1.3 77.8 - - + +
85A ARG* 1.3 72.9 + - - +
146A TYR* 4.5 2.8 - - - -
147A GLY* 3.3 30.1 - - - +
148A TYR 4.5 4.3 - - - -
149A THR* 3.5 37.2 - - - +
150A SER* 3.6 6.0 + - - +
252A ARG* 4.4 10.0 + - - -
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 2.8 27.5 + - - +
81A ASN* 3.2 53.3 + - - +
82A PHE* 3.1 5.3 + - - +
83A TRP 3.1 2.2 - - - -
84A THR* 1.3 91.4 - - - +
86A LYS* 1.3 63.4 + - - +
87A GLY 3.3 0.2 - - - -
146A TYR* 3.5 13.1 + - - -
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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