Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 1CCW
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 LEU 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.4 3.2 - - - +
70B ALA* 1.3 80.0 - - - +
72B LEU* 1.3 56.3 + - - +
73B ASP 3.5 0.7 - - - +
74B GLU* 3.3 35.2 + - + +
75B HIS* 2.7 37.3 + - - +
111B ILE* 3.5 44.4 - - + +
114B SER* 4.2 13.5 - - - +
115B GLU* 3.6 40.4 - - + +
118B GLY 6.4 0.2 - - - -
119B ARG 6.1 1.6 - - - +
120B SER* 5.7 0.9 - - - -
130B PHE* 3.9 3.1 - - + -
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Residues in contact with LEU 72 (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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71B LEU* 1.3 73.5 - - - +
73B ASP* 1.3 65.7 + - - +
75B HIS* 3.2 2.8 + - - +
76B ILE* 3.0 36.7 + - + +
125B PHE* 3.9 17.3 - - + -
130B PHE* 3.6 24.4 - - + -
134B GLY* 3.6 36.8 - - - +
137B LYS* 3.7 31.9 - - + +
138B VAL* 3.6 20.9 - - + -
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Residues in contact with ASP 73 (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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71B LEU 3.5 0.2 - - - -
72B LEU* 1.3 77.8 - - - +
74B GLU* 1.3 66.1 + - - +
76B ILE* 3.3 8.6 + - - +
77B GLU* 2.9 47.0 + - - +
137B LYS* 3.4 33.3 + - - -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.7 14.6 - - + +
71B LEU* 3.3 39.7 - - + +
73B ASP* 1.3 84.1 + - - +
75B HIS* 1.3 66.6 + - - +
77B GLU* 3.4 17.0 + - - +
78B LEU* 3.0 24.4 + - - +
115B GLU* 5.3 0.7 - - - +
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Residues in contact with HIS 75 (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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67B ALA 3.8 8.5 - - - -
68B GLY* 3.4 21.2 - - - -
69B VAL* 3.3 28.5 + - + +
71B LEU 2.7 21.8 + - - +
72B LEU 3.2 3.6 + - - +
74B GLU* 1.3 74.6 - - - +
76B ILE* 1.3 62.7 + - - +
78B LEU* 3.3 5.6 + - - +
79B LEU* 3.0 40.9 + - + +
93B SER* 3.3 27.3 + - - -
125B PHE* 3.4 39.4 - + + -
138B VAL* 4.1 18.6 - - + -
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Residues in contact with ILE 76 (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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72B LEU* 3.0 33.2 + - + +
73B ASP* 3.6 7.6 - - - +
74B GLU 3.3 0.2 - - - -
75B HIS* 1.3 78.4 - - - +
77B GLU* 1.3 63.3 + - + +
79B LEU* 3.3 5.5 + - - +
80B ARG* 3.0 40.9 + - + +
137B LYS* 3.7 43.3 - - + +
138B VAL* 3.9 24.2 - - + -
141B ALA* 3.5 23.8 - - + -
142B VAL* 5.1 1.1 - - + +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP* 2.9 39.3 + - - +
74B GLU* 3.8 16.5 - - - +
76B ILE* 1.3 78.6 - - + +
78B LEU* 1.3 64.3 + - - +
80B ARG* 3.5 11.6 + - - +
81B TYR* 3.0 24.1 + - - +
337B LYS* 5.2 3.3 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.0 13.5 - - + -
68B GLY* 4.0 27.1 - - - +
69B VAL* 4.1 23.6 - - + -
74B GLU 3.0 13.3 + - - +
75B HIS* 3.4 10.5 - - - +
77B GLU* 1.3 77.9 - - - +
79B LEU* 1.3 64.4 + - + +
81B TYR* 3.0 7.6 + - - +
82B LEU* 3.0 36.4 + - + +
335B PRO 5.6 2.5 - - - +
336B THR 5.2 0.9 - - - -
337B LYS* 3.6 37.0 - - + +
340B ASN* 5.4 2.7 - - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 4.0 25.4 - - + -
75B HIS* 3.0 42.2 + - + +
76B ILE* 3.3 3.8 + - - +
78B LEU* 1.3 78.3 - - + +
80B ARG* 1.3 58.3 + - - +
82B LEU* 3.2 10.8 + - + +
83B GLN* 2.9 29.2 + - - +
91B LEU* 3.8 13.6 - - + +
92B PRO* 3.5 32.1 - - + +
93B SER* 3.8 1.6 - - - +
138B VAL* 3.7 21.8 - - + -
142B VAL* 4.2 13.9 - - + -
146B LEU* 3.9 8.7 - - + -
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Residues in contact with ARG 80 (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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76B ILE* 3.0 34.1 + - + +
77B GLU* 3.7 11.8 - - - +
79B LEU* 1.3 76.5 - - - +
81B TYR* 1.3 58.8 + - - +
83B GLN* 4.2 11.0 - - - +
84B ASP* 2.8 44.3 + - - +
141B ALA* 3.0 45.7 + - - +
142B VAL* 4.4 6.9 - - + +
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Residues in contact with TYR 81 (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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77B GLU 3.0 14.0 + - - +
78B LEU 3.0 8.5 + - - +
80B ARG* 1.3 79.1 - - - +
82B LEU* 1.3 58.3 + - - +
84B ASP* 4.4 1.6 - - - +
85B GLU* 2.8 66.8 + - + +
86B GLY 3.1 4.3 + - - -
337B LYS* 3.5 69.3 - - + -
338B GLU* 3.8 17.3 + - + +
341B ALA* 3.7 8.7 - - + +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 3.8 16.2 - - + -
67B ALA* 3.5 32.3 - - + -
78B LEU* 3.0 24.3 + - + +
79B LEU* 3.2 12.5 + - + +
81B TYR* 1.3 75.7 - - + +
83B GLN* 1.3 61.9 + - - +
86B GLY* 3.2 6.8 - - - +
87B GLY 3.1 17.7 + - - -
88B ALA* 3.1 11.4 + - + +
91B LEU* 4.3 8.1 - - + -
337B LYS* 3.9 13.7 - - - +
340B ASN* 3.7 35.9 - - + +
341B ALA* 3.9 7.6 - - - +
344B ILE* 4.0 10.6 - - + +
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Residues in contact with GLN 83 (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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79B LEU 2.9 16.9 + - - +
80B ARG* 3.5 8.6 + - - +
82B LEU* 1.3 76.6 - - - +
84B ASP* 1.3 80.8 + - - +
87B GLY* 3.2 22.2 + - - -
88B ALA* 3.8 3.8 + - - +
91B LEU* 3.9 3.2 - - + +
141B ALA 5.1 2.2 + - - -
142B VAL* 3.6 15.1 - - - +
143B ASN* 2.8 43.2 + - - +
144B LEU* 3.7 32.9 - - + +
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Residues in contact with ASP 84 (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 ARG* 2.8 28.9 + - - +
81B TYR* 4.8 1.3 - - - -
83B GLN* 1.3 102.1 + - - +
85B GLU* 1.3 63.2 + - + +
87B GLY* 4.1 3.5 + - - -
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Residues in contact with GLU 85 (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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81B TYR* 2.8 60.9 + - + +
84B ASP* 1.3 76.8 - - + +
86B GLY* 1.3 61.2 + - - +
341B ALA* 4.1 6.5 - - + -
345B LYS* 3.1 38.5 + - - +
300D ASP* 4.7 0.7 - - - +
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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