Contacts of the helix formed by residues 68 - 87 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLN* 4.9 2.9 + - + +
62C ASP* 5.8 3.4 - - + +
65C LEU* 3.3 26.8 + - + +
66C ARG 3.1 2.8 + - - -
67C ASN* 1.3 75.7 - - - +
69C LYS* 1.3 57.9 + - + +
72C ALA* 2.8 34.5 + - + +
138C ILE* 3.7 14.8 - - + -
151C HIS* 3.7 37.2 - - + +
153C ALA* 3.8 14.8 - - + -
154C LEU* 3.6 36.1 - - + -
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLU* 4.2 31.5 + - + +
60C GLN* 6.1 3.3 - - + +
67C ASN* 3.3 0.8 - - - -
68C LEU* 1.3 80.7 - - + +
70C ALA* 1.3 57.7 + - - +
72C ALA* 3.9 3.1 - - - +
73C GLU* 3.0 32.2 + - + +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.2 30.4 - - + +
51C ILE* 4.9 1.0 - - - +
52C GLY* 4.1 14.6 + - - +
53C LYS 4.5 3.4 - - - +
54C ALA* 4.2 17.5 - - + +
67C ASN* 3.3 5.4 + - - +
69C LYS* 1.3 76.7 - - - +
71C VAL* 1.3 61.3 + - - +
73C GLU* 4.1 4.1 - - - +
74C ALA* 3.1 30.8 + - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C MET* 3.9 9.1 - - + +
13C LEU* 3.5 40.6 - - + +
14C GLY* 4.2 2.0 - - - +
67C ASN 2.9 22.2 + - - +
68C LEU 4.0 2.2 - - - +
70C ALA* 1.3 76.8 - - - +
72C ALA* 1.3 58.6 + - - +
74C ALA* 3.9 1.2 - - - +
75C ASN* 2.9 51.0 + - - +
100C SER* 3.8 13.2 - - - +
138C ILE* 3.9 31.2 - - + -
154C LEU* 4.5 3.6 - - + -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 2.8 22.4 + - + +
69C LYS* 3.9 3.6 - - - +
71C VAL* 1.3 77.7 - - - +
73C GLU* 1.3 57.5 + - - +
75C ASN* 3.4 1.3 + - - -
76C GLU* 3.0 25.6 + - - +
153C ALA* 3.6 28.7 - - + +
154C LEU* 4.3 11.0 - - + -
157C ILE* 3.4 18.0 - - + +
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 3.0 18.6 + - + +
70C ALA* 4.2 3.6 - - - +
72C ALA* 1.3 74.6 - - - +
74C ALA* 1.3 65.5 + - - +
76C GLU* 3.1 31.6 + - - +
77C LYS* 3.2 36.6 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 5.6 1.5 - - - +
11C MET* 3.7 15.7 - - + -
49C ILE* 3.8 3.8 - - - +
50C PRO 4.6 2.7 - - - +
51C ILE* 3.6 35.7 - - + -
52C GLY 5.4 0.9 - - - +
70C ALA 3.1 20.4 + - - +
73C GLU* 1.3 75.8 - - - +
75C ASN* 1.3 58.2 + - - +
77C LYS* 3.1 17.7 + - - +
78C LEU* 2.9 26.6 + - - +
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C MET* 4.2 6.1 - - - +
71C VAL* 2.9 39.8 + - - +
72C ALA* 3.7 6.0 - - - +
73C GLU 3.2 0.2 - - - -
74C ALA* 1.3 73.8 - - - +
76C GLU* 1.3 60.5 + - - +
78C LEU* 3.7 5.7 - - - +
79C ALA* 2.9 29.3 + - - +
100C SER 3.1 25.9 + - - +
101C ILE* 3.3 12.0 - - - +
103C ILE* 4.0 9.5 - - + +
104C GLY* 2.8 33.5 + - - +
154C LEU* 5.2 0.4 - - - +
157C ILE* 3.7 13.6 - - + +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA 3.0 17.7 + - - +
73C GLU* 3.1 30.9 + - - +
75C ASN* 1.3 75.3 - - - +
77C LYS* 1.3 65.6 + - - +
79C ALA* 3.3 5.0 + - - +
80C ALA* 3.1 21.7 + - - +
156C GLN 4.3 1.9 - - - +
157C ILE* 3.2 32.2 - - + +
158C GLY* 3.2 18.8 + - - -
159C GLY 5.0 0.2 + - - -
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.6 15.9 - - + +
50C PRO* 3.4 39.3 + - + +
52C GLY 5.1 5.9 - - - +
73C GLU* 3.4 38.8 + - - +
74C ALA* 3.1 8.6 + - - +
76C GLU* 1.3 77.6 - - - +
78C LEU* 1.3 62.9 + - - +
80C ALA* 3.2 8.1 + - - +
81C ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.9 16.2 - - + -
9C VAL* 3.7 28.5 - - + -
49C ILE* 4.1 11.8 - - + +
74C ALA 2.9 15.8 + - - +
75C ASN* 3.7 8.3 - - - +
76C GLU 3.3 0.2 - - - -
77C LYS* 1.3 77.4 - - - +
79C ALA* 1.3 52.0 + - - +
81C ALA* 3.1 1.4 + - - +
82C VAL* 2.8 55.5 + - + +
94C VAL* 4.4 4.5 - - + -
101C ILE* 3.2 40.4 - - + +
104C GLY* 3.8 2.7 - - - -
105C THR* 3.4 22.2 - - - +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASN 2.9 18.3 + - - +
76C GLU* 3.5 8.5 - - - +
77C LYS 3.3 0.2 - - - -
78C LEU* 1.3 75.8 - - - +
80C ALA* 1.3 58.6 + - - +
82C VAL* 3.3 0.8 + - - -
83C ASP* 2.8 31.7 + - - +
104C GLY 3.3 20.6 - - - +
107C ALA* 3.7 19.1 - - + +
108C GLY* 3.5 7.9 - - - +
111C LYS* 6.1 1.3 - - - +
157C ILE* 4.2 6.5 - - + -
158C GLY* 5.0 5.4 - - - -
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLU 3.1 10.3 + - - +
77C LYS* 3.5 10.5 - - - +
78C LEU 3.2 0.2 - - - -
79C ALA* 1.3 79.4 - - - +
81C ALA* 1.3 63.7 + - - +
83C ASP* 3.2 8.1 + - - +
84C GLN* 3.0 24.5 + - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 3.9 15.9 - - + -
46C LEU* 5.9 0.9 - - + -
49C ILE* 3.8 21.1 - - + -
77C LYS 3.0 13.0 + - - +
78C LEU 3.5 7.2 - - - +
80C ALA* 1.3 77.6 - - - +
82C VAL* 1.3 61.1 + - - +
84C GLN* 3.2 19.8 + - - +
85C VAL* 3.1 22.0 + - - +
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ILE* 4.0 10.5 - - + -
78C LEU* 2.8 46.0 + - + +
79C ALA* 3.8 3.4 - - - +
81C ALA* 1.3 73.4 - - - +
83C ASP* 1.3 62.3 + - - +
85C VAL* 3.2 5.4 + - - +
86C VAL* 3.1 21.0 + - - +
92C PRO* 3.9 13.7 - - + -
94C VAL* 3.9 18.2 - - + -
105C THR* 3.8 12.8 - - + +
108C GLY* 4.1 6.3 - - - -
109C VAL* 3.5 31.9 - - + -
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 2.8 21.9 + - - +
80C ALA* 3.2 9.5 + - - +
82C VAL* 1.3 73.1 - - - +
84C GLN* 1.3 57.9 + - - +
86C VAL* 3.2 4.7 + - - +
87C GLN* 2.9 43.8 + - - +
108C GLY* 3.5 15.9 + - - +
111C LYS* 3.6 24.8 + - - +
112C HIS* 2.6 33.7 + - - -
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Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 4.0 12.2 - - - +
80C ALA 3.0 12.4 + - - +
81C ALA* 3.2 26.1 + - - +
82C VAL 3.3 0.2 - - - -
83C ASP* 1.3 76.4 - - - +
85C VAL* 1.3 68.8 + - - +
87C GLN* 3.1 15.8 + - - +
88C ARG* 2.9 61.5 + - + +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C SER* 3.6 28.7 - - - +
7C ILE* 4.0 9.0 - - + -
46C LEU* 3.4 31.9 - - + -
81C ALA 3.1 12.4 + - - +
82C VAL 3.2 7.4 + - - +
84C GLN* 1.3 80.8 - - - +
86C VAL* 1.3 62.8 + - - +
88C ARG* 3.2 15.2 + - - +
89C GLY 3.5 0.2 + - - -
90C ARG* 3.1 35.1 + - + +
92C PRO* 4.0 17.7 - - + -
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Residues in contact with VAL 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C VAL* 3.1 18.4 + - + +
83C ASP 3.5 6.3 - - - +
85C VAL* 1.3 74.3 - - - +
87C GLN* 1.3 63.3 + - - +
89C GLY* 2.9 15.8 + - - -
90C ARG 3.9 9.1 + - - +
92C PRO* 4.2 23.8 - - + -
108C GLY 4.2 11.4 - - - +
109C VAL* 4.4 8.5 - - + -
112C HIS* 3.5 36.6 - - + +
113C TYR* 5.0 10.3 - - + +
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Residues in contact with GLN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 2.9 40.6 + - - +
84C GLN* 3.1 15.8 + - - +
86C VAL* 1.3 77.3 - - - +
88C ARG* 1.3 58.7 + - + +
89C GLY* 3.2 4.3 + - - -
111C LYS* 5.6 0.6 - - - +
112C HIS* 3.7 15.8 - - + -
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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