Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 4CEV
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.3 1.0 + - - +
60A GLN* 4.9 2.6 + - + +
62A ASP* 5.6 3.8 - - + +
65A LEU* 3.4 25.9 + - + +
66A ARG 3.1 2.4 + - - -
67A ASN* 1.3 76.3 - - - +
69A LYS* 1.3 65.2 + - + +
72A ALA* 2.8 33.1 + - - +
138A ILE* 3.7 14.4 - - + -
151A HIS* 3.7 37.7 - - + +
153A ALA* 4.0 14.4 - - + -
154A LEU* 3.6 36.8 - - + -
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 4.0 24.6 + - - +
67A ASN 3.3 0.4 - - - -
68A LEU* 1.3 84.7 - - + +
70A ALA* 1.3 58.3 + - - +
72A ALA* 3.3 4.8 + - - +
73A GLU* 2.8 32.6 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.3 29.9 - - + +
51A ILE* 5.1 0.9 - - - +
52A GLY* 3.6 16.8 + - - +
53A LYS 4.4 2.0 - - - +
54A ALA* 4.0 17.3 - - + +
55A GLU* 6.4 0.2 - - - +
67A ASN 3.3 5.3 + - - +
69A LYS* 1.3 75.3 - - - +
71A VAL* 1.3 57.8 + - - +
73A GLU* 3.4 4.8 + - - +
74A ALA* 3.0 31.2 + - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 3.8 9.4 - - + -
13A LEU* 3.6 38.8 - - + +
14A GLY* 4.3 2.5 - - - +
67A ASN 2.9 24.0 + - - +
68A LEU 3.9 2.5 - - - +
70A ALA* 1.3 74.6 - - - +
72A ALA* 1.3 65.0 + - - +
74A ALA* 3.9 1.4 - - - +
75A ASN* 3.0 45.2 + - - +
100A SER* 3.8 9.9 - - - +
138A ILE* 3.7 35.7 - - + -
154A LEU* 4.3 4.7 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU 2.8 19.9 + - - +
69A LYS* 3.7 4.7 - - - +
71A VAL* 1.3 80.1 - - - +
73A GLU* 1.3 61.4 + - - +
75A ASN* 4.6 0.2 - - - -
76A GLU* 3.1 20.2 + - - +
153A ALA* 3.7 31.2 - - + +
154A LEU* 4.4 10.5 - - + -
157A ILE* 3.3 17.3 - - + +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS 2.8 17.8 + - - +
70A ALA* 3.9 5.8 - - - +
72A ALA* 1.3 75.2 - - - +
74A ALA* 1.3 64.8 + - - +
76A GLU* 3.0 29.4 + - - +
77A LYS* 3.1 41.7 + - - +
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Residues in contact with ALA 74 (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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9A VAL* 5.6 2.0 - - + -
11A MET* 3.6 17.5 - - + -
49A ILE* 3.8 4.4 - - - +
51A ILE* 3.5 37.2 - - + -
52A GLY 5.4 0.4 - - - +
70A ALA 3.0 18.4 + - - +
73A GLU* 1.3 76.6 - - - +
75A ASN* 1.3 58.0 + - - +
77A LYS* 3.2 15.8 + - - +
78A LEU* 2.9 27.3 + - - +
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Residues in contact with ASN 75 (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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11A MET* 4.2 5.2 - - - +
71A VAL* 3.0 38.8 + - - +
72A ALA* 3.8 5.3 - - - +
74A ALA* 1.3 74.8 - - - +
76A GLU* 1.3 61.3 + - - +
78A LEU* 3.7 6.9 - - - +
79A ALA* 2.9 29.1 + - - +
100A SER 3.1 24.6 + - - +
101A ILE* 3.3 13.2 - - - +
103A ILE* 3.9 9.4 - - + +
104A GLY* 2.8 33.5 + - - +
154A LEU* 5.1 0.8 - - - +
157A ILE* 3.6 14.9 - - + +
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Residues in contact with GLU 76 (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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72A ALA 3.1 15.5 + - - +
73A GLU* 3.0 30.2 + - - +
75A ASN* 1.3 73.4 - - - +
77A LYS* 1.3 67.3 + - + +
79A ALA* 3.3 3.5 + - - +
80A ALA* 3.1 22.0 + - - +
156A GLN 4.4 1.7 - - - +
157A ILE* 3.3 21.7 - - + +
158A GLY* 3.3 26.9 + - - -
159A GLY 4.9 0.3 + - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.7 14.6 - - + +
50A PRO* 3.3 40.8 + - + +
52A GLY* 5.2 5.1 - - - +
73A GLU* 3.1 44.2 + - - +
74A ALA* 3.2 8.2 + - - +
76A GLU* 1.3 77.8 - - + +
78A LEU* 1.3 62.7 + - - +
80A ALA* 3.2 8.4 + - - +
81A ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 7.9 - - + -
9A VAL* 3.7 27.1 - - + -
49A ILE* 4.1 19.5 - - + +
74A ALA 2.9 16.1 + - - +
75A ASN* 3.7 9.4 - - - +
77A LYS* 1.3 77.4 - - - +
79A ALA* 1.3 63.7 + - - +
81A ALA* 3.2 1.2 + - - +
82A VAL* 2.9 43.9 + - + +
94A VAL* 4.1 6.7 - - + -
101A ILE* 3.1 37.9 - - + +
104A GLY* 3.6 7.0 - - - -
105A THR* 3.2 19.5 - - - +
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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
----------------------------------------------------------
75A ASN 2.9 19.2 + - - +
76A GLU* 3.6 7.6 - - - +
78A LEU* 1.3 76.9 - - - +
80A ALA* 1.3 57.4 + - - +
82A VAL* 4.6 0.2 - - - -
83A ASP* 2.9 30.9 + - - +
104A GLY 3.2 20.4 - - - +
107A ALA* 3.7 20.0 - - + -
108A GLY* 3.5 7.8 - - - +
111A LYS* 6.2 0.2 - - - -
157A ILE* 4.1 6.3 - - + -
158A GLY* 5.0 6.1 - - - -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU 3.1 12.8 + - - +
77A LYS* 3.5 10.8 - - - +
79A ALA* 1.3 74.3 - - - +
81A ALA* 1.3 66.2 + - - +
83A ASP* 3.2 8.1 + - - +
84A GLN* 3.0 24.0 + - - +
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Residues in contact with ALA 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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7A ILE* 3.9 15.7 - - + -
46A LEU* 5.2 2.8 - - + +
49A ILE* 3.8 21.5 - - + -
77A LYS 3.0 12.2 + - - +
78A LEU* 3.2 7.2 + - - +
80A ALA* 1.3 76.4 - - - +
82A VAL* 1.3 61.9 + - - +
84A GLN* 3.5 8.2 + - - +
85A VAL* 3.3 25.8 + - - +
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Residues in contact with VAL 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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7A ILE* 4.1 11.0 - - + -
78A LEU* 2.9 43.3 + - + +
79A ALA* 3.8 3.1 - - - +
81A ALA* 1.3 73.0 - - - +
83A ASP* 1.3 65.5 + - - +
85A VAL* 3.3 4.3 + - - +
86A VAL* 3.1 22.9 + - + +
92A PRO* 4.1 11.0 - - + -
94A VAL* 4.0 17.5 - - + -
105A THR* 3.7 14.1 - - + +
108A GLY* 3.9 7.4 - - - -
109A VAL* 3.5 32.5 - - + -
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Residues in contact with ASP 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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79A ALA 2.9 18.6 + - - +
80A ALA* 3.5 8.3 - - - +
82A VAL* 1.3 76.8 - - - +
84A GLN* 1.3 59.4 + - - +
86A VAL 3.4 1.2 + - - -
87A GLN* 3.0 47.7 + - - +
108A GLY* 3.5 14.1 - - - +
111A LYS* 3.1 29.8 + - - +
112A HIS* 2.7 30.1 + - - -
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Residues in contact with GLN 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 ALA 3.0 16.0 + - - +
81A ALA* 3.9 7.6 + - - +
83A ASP* 1.3 77.6 - - - +
85A VAL* 1.3 57.1 + - + +
87A GLN* 3.1 17.9 + - - +
88A ARG* 2.8 55.7 + - + +
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Residues in contact with VAL 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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5A SER* 3.7 23.8 - - - +
7A ILE* 4.0 9.0 - - + -
46A LEU* 3.4 31.4 - - + -
81A ALA 3.3 14.4 + - - +
82A VAL* 3.3 9.2 + - - +
84A GLN* 1.3 73.0 - - + +
86A VAL* 1.3 66.4 + - - +
88A ARG* 3.1 19.5 + - - +
90A ARG* 3.0 42.9 + - + +
92A PRO* 3.9 17.0 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL 3.1 17.4 + - - +
83A ASP 3.6 6.1 - - - +
85A VAL* 1.3 76.0 - - - +
87A GLN* 1.3 58.7 + - - +
89A GLY* 2.8 22.0 + - - -
90A ARG 3.8 7.8 - - - +
92A PRO* 4.2 24.7 - - + -
108A GLY 4.3 0.2 - - - +
109A VAL* 4.3 13.5 - - + -
112A HIS* 3.5 42.0 - - + +
113A TYR* 5.1 9.4 - - + +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 3.0 42.9 + - - +
84A GLN* 3.4 21.7 - - + +
86A VAL* 1.3 79.6 - - - +
88A ARG* 1.3 58.5 + - + +
89A GLY* 3.1 4.7 + - - -
111A LYS* 5.4 1.4 - - - +
112A HIS* 3.7 15.4 - - + -
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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
------------------------------------------------------------
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