Contacts of the helix formed by residues 68 - 87 (chain B) in PDB entry 5CEV
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 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY 4.9 10.8 - - - +
62B ASP* 4.3 1.8 - - - +
65B LEU* 3.3 25.0 + - + +
66B ARG 3.1 3.0 + - - -
67B ASN* 1.3 75.2 - - - +
69B LYS* 1.3 58.3 + - - +
71B VAL* 3.7 0.7 - - - +
72B ALA* 2.8 32.7 + - - +
138B ILE* 3.8 11.7 - - + -
151B HIS* 3.4 40.8 - - + +
153B ALA* 4.0 13.5 - - + -
154B LEU* 3.8 36.6 - - + -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU* 5.9 8.3 - - + -
60B GLN* 4.1 34.9 + - + -
67B ASN 3.4 0.6 - - - -
68B LEU* 1.3 79.5 - - - +
70B ALA* 1.3 57.9 + - - +
72B ALA* 3.3 4.8 + - - +
73B GLU* 2.8 60.8 + - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.5 27.1 - - + +
52B GLY* 5.0 7.4 + - - -
53B LYS 4.3 18.2 - - - +
54B ALA* 5.1 1.8 - - - -
55B GLU 5.8 0.7 - - - +
67B ASN* 3.2 13.0 + - + +
69B LYS* 1.3 78.6 - - - +
71B VAL* 1.3 60.5 + - - +
73B GLU* 4.0 9.2 - - - +
74B ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 4.0 8.5 - - + -
13B LEU* 3.5 39.0 - - + +
14B GLY* 4.0 2.7 - - - +
67B ASN 2.8 26.4 + - - +
68B LEU 3.8 2.9 - - - +
70B ALA* 1.3 69.8 - - - +
72B ALA* 1.3 66.3 + - - +
74B ALA* 3.9 1.0 - - - +
75B ASN* 2.9 47.1 + - - +
100B SER* 3.9 13.9 - - - +
138B ILE* 4.0 29.8 - - + -
154B LEU* 4.4 6.1 - - + -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 2.8 19.5 + - - +
69B LYS* 3.6 5.2 - - - +
71B VAL* 1.3 77.6 - - - +
73B GLU* 1.3 63.5 + - + +
75B ASN* 3.2 2.0 + - - -
76B GLU* 3.0 22.3 + - + +
153B ALA* 3.7 32.3 - - + +
154B LEU* 4.5 7.0 - - + -
157B ILE* 3.3 16.7 - - + +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 2.8 50.3 + - + +
70B ALA* 4.1 6.7 - - - +
72B ALA* 1.3 75.4 - - + +
74B ALA* 1.3 62.2 + - - +
76B GLU* 3.2 10.5 + - + +
77B LYS* 3.2 36.4 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.8 1.3 - - + -
11B MET* 3.7 17.5 - - + -
49B ILE* 3.9 3.6 - - - +
50B PRO 4.7 6.1 - - - +
51B ILE* 3.6 35.4 - - + -
52B GLY 5.3 1.1 - - - +
70B ALA 3.1 19.0 + - - +
73B GLU* 1.3 75.6 - - - +
75B ASN* 1.3 59.5 + - - +
77B LYS* 3.2 11.8 + - - +
78B LEU* 2.9 26.6 + - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B MET* 4.1 7.4 - - - +
71B VAL* 2.9 43.6 + - - +
72B ALA* 3.7 4.0 - - - +
74B ALA* 1.3 75.9 - - - +
76B GLU* 1.3 59.4 + - - +
78B LEU* 3.3 5.8 + - - +
79B ALA* 2.8 30.3 + - - +
100B SER 3.3 19.5 + - - +
101B ILE* 3.4 11.7 - - - +
103B ILE* 4.0 9.0 - - - +
104B GLY* 2.9 33.4 + - - +
154B LEU* 5.2 0.6 - - - +
157B ILE* 3.7 16.3 - - + +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 3.0 17.6 + - - +
73B GLU* 3.4 11.9 - - - +
75B ASN* 1.3 74.7 - - - +
77B LYS* 1.3 65.8 + - + +
79B ALA* 3.2 4.9 + - - +
80B ALA* 3.1 21.7 + - - +
156B GLN 4.1 2.1 - - - +
157B ILE* 3.2 36.2 - - + +
158B GLY* 3.3 16.7 + - - -
159B GLY 4.9 0.3 + - - -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.7 15.3 - - + +
50B PRO* 3.8 39.4 + - + +
73B GLU* 3.2 26.0 + - - +
74B ALA* 3.2 9.1 + - - +
76B GLU* 1.3 81.0 - - + +
78B LEU* 1.3 61.3 + - - +
80B ALA* 3.2 8.6 + - - +
81B ALA* 3.1 22.0 + - - +
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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
----------------------------------------------------------
7B ILE* 4.0 17.5 - - + -
9B VAL* 3.7 35.2 - - + -
49B ILE* 3.9 12.0 - - + +
74B ALA 2.9 13.4 + - - +
75B ASN* 3.6 11.2 - - - +
77B LYS* 1.3 75.3 - - - +
79B ALA* 1.3 64.4 + - - +
81B ALA* 3.1 2.1 + - - +
82B VAL* 2.8 42.8 + - + +
94B VAL* 4.3 4.5 - - + -
101B ILE* 3.3 35.7 - - + +
104B GLY* 4.0 2.0 - - - -
105B THR* 3.7 17.9 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN 2.8 18.3 + - - +
76B GLU* 3.5 7.6 - - - +
78B LEU* 1.3 76.8 - - - +
80B ALA* 1.3 56.6 + - - +
82B VAL 3.4 0.2 + - - -
83B ASP* 2.9 30.8 + - - +
104B GLY 3.3 20.5 + - - +
107B ALA* 3.7 20.6 - - + -
108B GLY* 3.4 8.3 - - - +
157B ILE* 4.0 7.6 - - + -
158B GLY* 4.8 5.8 - - - -
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 3.1 12.0 + - - +
77B LYS* 3.2 11.2 + - - +
79B ALA* 1.3 75.1 - - - +
81B ALA* 1.3 63.0 + - - +
83B ASP* 3.3 8.1 + - - +
84B GLN* 3.0 26.9 + - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.8 15.7 - - + -
46B LEU* 5.3 1.7 - - + +
49B ILE* 3.8 21.3 - - + -
77B LYS 3.1 12.4 + - - +
78B LEU 3.5 7.4 - - - +
80B ALA* 1.3 77.1 - - - +
82B VAL* 1.3 62.6 + - - +
84B GLN* 3.4 6.4 + - - +
85B VAL* 3.2 25.6 + - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.9 14.4 - - + -
78B LEU* 2.8 40.5 + - + +
79B ALA* 3.9 3.6 - - - +
81B ALA* 1.3 74.4 - - - +
83B ASP* 1.3 62.9 + - - +
85B VAL* 3.2 5.8 + - - +
86B VAL* 3.0 26.6 + - + +
92B PRO* 4.1 10.8 - - + -
94B VAL* 4.0 15.5 - - + -
105B THR* 3.8 11.4 - - + +
108B GLY* 3.8 11.7 - - - -
109B VAL* 3.4 33.0 - - + -
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Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 2.9 18.9 + - - +
80B ALA* 3.4 9.1 - - - +
82B VAL* 1.3 77.3 - - - +
84B GLN* 1.3 57.9 + - - +
86B VAL* 3.2 3.1 + - - +
87B GLN* 2.8 43.8 + - - +
108B GLY* 3.5 15.5 + - - +
111B LYS* 2.7 27.9 + - - -
112B HIS* 2.7 32.1 + - - -
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Residues in contact with GLN 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 ALA 3.0 17.6 + - - +
81B ALA* 3.6 8.1 - - - +
83B ASP* 1.3 75.8 - - - +
85B VAL* 1.3 52.0 + - + +
87B GLN* 2.9 35.1 + - - +
88B ARG* 2.8 55.1 + - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER* 3.5 27.8 - - - +
7B ILE* 4.2 8.5 - - + -
46B LEU* 3.4 33.7 - - + -
81B ALA 3.2 11.9 + - - +
82B VAL 3.2 8.0 + - - +
84B GLN* 1.3 75.5 - - + +
86B VAL* 1.3 62.9 + - - +
88B ARG* 3.1 19.7 + - - +
89B GLY 3.4 0.2 + - - -
90B ARG* 3.1 41.7 + - + +
92B PRO* 4.0 16.4 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.0 19.5 + - + +
83B ASP 3.6 5.8 - - - +
85B VAL* 1.3 75.4 - - - +
87B GLN* 1.3 57.9 + - - +
89B GLY* 2.9 21.0 + - - -
90B ARG 3.8 7.6 - - - +
92B PRO* 4.1 25.4 - - + -
108B GLY 4.3 9.4 - - - +
109B VAL* 4.4 8.1 - - + -
112B HIS* 3.6 37.0 - - + +
113B TYR* 5.1 10.5 - - + +
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 2.8 43.3 + - - +
84B GLN* 2.9 35.3 + - - +
86B VAL* 1.3 78.6 - - - +
88B ARG* 1.3 55.3 - - + +
89B GLY 3.2 4.2 + - - -
111B LYS* 4.6 4.0 - - - +
112B HIS* 3.9 12.1 - - + -
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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
------------------------------------------------------------
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