Contacts of the helix formed by residues 86 - 104 (chain C) in PDB entry 1VI9
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 SER 86 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ASP* 5.7 9.4 - - - -
57C PRO* 4.6 2.6 - - - +
84C LEU* 3.4 9.4 - - - +
85C GLY* 1.3 79.7 - - - +
87C ALA* 1.3 61.1 + - - +
88C GLU* 3.3 11.3 + - - +
89C GLN* 2.9 30.6 + - - +
90C GLY* 3.2 15.2 + - - -
125C ALA* 5.6 1.1 - - - -
128C VAL* 3.7 10.9 - - - +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP* 5.5 2.4 + - - +
86C SER* 1.3 72.0 - - - +
88C GLU* 1.3 61.4 + - - +
90C GLY* 3.2 2.4 + - - +
91C GLU* 2.9 29.5 + - - +
127C GLY* 3.6 31.9 - - - +
128C VAL* 4.1 3.0 - - - +
131C PHE* 4.3 16.2 - - + -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PRO* 3.9 21.1 - - + +
86C SER* 3.2 9.9 + - - +
87C ALA* 1.3 77.7 - - - +
89C GLN* 1.3 65.1 + - - +
91C GLU* 3.3 5.8 + - + +
92C HIS* 3.1 49.8 + - + +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C THR* 3.5 33.3 + - - +
39C VAL* 5.2 1.6 - - - +
54C VAL* 4.1 22.6 - - + +
55C MSE 4.4 2.6 + - - -
57C PRO* 4.0 21.7 - - + +
60C LEU* 4.4 12.5 - - + +
83C TYR 4.7 1.6 - - - +
84C LEU* 3.7 12.1 - - + +
85C GLY* 2.8 30.5 + - - +
86C SER* 2.9 22.5 + - - +
88C GLU* 1.3 77.7 - - - +
90C GLY* 1.3 62.3 + - - +
92C HIS* 3.4 3.3 + - - +
93C ILE* 3.0 29.3 + - + +
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.9 19.2 - - - +
86C SER 3.2 5.0 + - - -
87C ALA 3.2 7.8 + - - -
89C GLN* 1.3 79.8 - - - +
91C GLU* 1.3 55.0 + - - +
93C ILE* 3.2 6.1 + - - +
94C LEU* 2.9 31.4 + - - +
131C PHE* 3.5 23.5 - - - -
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Residues in contact with GLU 91 (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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87C ALA 2.9 15.1 + - - +
88C GLU* 3.7 8.7 - - + +
90C GLY* 1.3 71.5 - - - +
92C HIS* 1.3 64.7 + - + +
94C LEU* 3.1 12.4 + - - +
95C GLY* 2.8 26.3 + - - -
98C ARG* 3.6 22.7 + - - +
131C PHE* 3.8 11.6 - - - -
135C HIS* 3.7 26.7 + - - -
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Residues in contact with HIS 92 (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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57C PRO* 3.2 28.6 + - + +
58C SER* 3.7 24.0 + - - -
60C LEU* 4.8 4.7 - - + -
61C THR* 2.6 30.0 + - + +
88C GLU* 3.1 44.8 + - + +
89C GLN 3.8 4.5 - - - +
90C GLY 3.3 0.2 - - - -
91C GLU* 1.3 78.7 - - + +
93C ILE* 1.3 57.9 + - - +
95C GLY* 3.1 3.0 + - - +
96C ILE* 2.8 33.8 + - - +
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Residues in contact with ILE 93 (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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8C ILE* 3.8 45.1 - - + +
38C THR* 5.3 2.5 - - + -
60C LEU* 4.5 8.7 - - + -
79C VAL* 4.7 1.1 - - + -
81C SER* 4.3 14.6 - - - -
84C LEU* 3.4 33.2 - - + -
89C GLN* 3.0 17.2 + - + +
90C GLY* 3.5 8.1 - - - +
92C HIS* 1.3 77.4 - - - +
94C LEU* 1.3 58.6 + - + +
96C ILE* 3.1 10.2 + - + +
97C VAL* 2.8 30.6 + - + +
109C TYR* 4.3 25.8 - - + +
131C PHE* 6.1 0.4 - - + -
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Residues in contact with LEU 94 (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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90C GLY 2.9 16.0 + - - +
91C GLU* 3.1 14.5 + - - +
93C ILE* 1.3 74.3 - - + +
95C GLY* 1.3 65.8 + - - +
97C VAL* 3.8 6.0 - - + +
98C ARG* 3.0 40.9 + - - +
109C TYR* 3.6 27.8 - - + +
131C PHE* 3.4 29.4 - - + -
135C HIS* 3.7 26.7 - - + +
136C GLY* 4.3 1.6 - - - -
139C ALA* 3.6 25.8 - - + -
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Residues in contact with GLY 95 (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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91C GLU 2.8 15.0 + - - -
92C HIS* 3.1 4.7 + - - -
94C LEU* 1.3 77.9 - - - +
96C ILE* 1.3 60.0 + - - +
98C ARG* 3.4 23.0 + - - +
99C GLN* 3.1 24.8 + - - +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.7 27.1 - - + -
8C ILE* 4.0 21.8 - - + -
36C LEU* 4.3 0.7 - - + -
60C LEU* 3.9 37.7 - - + +
61C THR* 4.2 9.0 - - + +
64C VAL* 3.8 22.4 - - + +
79C VAL* 4.4 2.9 - - + -
92C HIS 2.8 19.0 + - - +
93C ILE* 3.3 11.4 - - + +
95C GLY* 1.3 73.9 - - - +
97C VAL* 1.3 61.1 + - - +
99C GLN* 3.1 11.0 + - - +
100C VAL* 2.9 33.1 + - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 3.8 25.6 - - + -
93C ILE* 2.8 23.6 + - + +
94C LEU* 3.8 8.1 - - + +
96C ILE* 1.3 68.5 - - - +
98C ARG* 1.3 67.8 + - + +
100C VAL* 3.3 2.0 + - + +
101C LYS* 2.9 43.1 + - + +
108C LYS 5.8 0.2 - - - -
109C TYR* 3.6 54.5 - - + -
139C ALA* 5.0 5.4 - - + +
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Residues in contact with ARG 98 (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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91C GLU* 3.6 23.8 + - - +
94C LEU* 3.0 25.6 + - - +
95C GLY* 3.5 31.0 - - - +
97C VAL* 1.3 78.4 - - + +
99C GLN* 1.3 63.1 + - - +
101C LYS* 3.2 6.9 + - - +
102C ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 99 (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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61C THR* 5.6 1.2 - - - +
64C VAL* 3.7 18.3 - - + +
65C GLN* 3.4 29.2 + - - +
68C ALA* 3.8 21.3 - - - +
73C LEU* 3.4 14.1 - - + -
95C GLY 3.1 12.7 + - - +
96C ILE* 3.5 11.9 - - - +
98C ARG* 1.3 81.5 - - - +
100C VAL* 1.3 61.7 + - - +
102C ALA* 3.4 6.9 + - - +
103C ALA* 3.1 22.0 + - - +
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Residues in contact with VAL 100 (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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6C LEU* 4.7 2.5 - - + -
73C LEU* 4.2 29.8 - - + +
76C CYS* 3.6 29.4 - - + +
79C VAL* 3.8 23.8 - - + -
96C ILE* 2.9 27.6 + - + +
97C VAL* 3.7 4.7 - - + +
99C GLN* 1.3 73.1 - - - +
101C LYS* 1.3 52.4 + - + +
103C ALA* 3.0 3.5 + - - +
104C ASN* 2.6 34.3 + - - +
107C ALA* 3.4 26.5 - - + -
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Residues in contact with LYS 101 (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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97C VAL* 2.9 40.0 + - + +
98C ARG* 3.8 5.6 - - - +
100C VAL* 1.3 76.3 - - + +
102C ALA* 1.3 59.2 + - - +
104C ASN 3.4 7.0 - - - +
105C PRO* 3.0 37.4 - - + +
107C ALA* 3.6 25.7 + - + +
108C LYS 4.8 0.2 - - - -
109C TYR* 4.5 2.9 - - - +
139C ALA 4.1 10.3 + - - -
141C ASP* 2.8 36.9 + - - -
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Residues in contact with ALA 102 (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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98C ARG 3.0 17.4 + - - +
99C GLN* 3.7 7.6 - - - +
101C LYS* 1.3 76.1 - - - +
103C ALA* 1.3 61.4 + - - +
105C PRO* 4.4 6.6 - - - +
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Residues in contact with ALA 103 (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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73C LEU* 3.9 16.8 - - + -
74C HIS* 3.5 38.0 - - + +
99C GLN 3.1 12.3 + - - +
100C VAL 3.0 7.5 + - - +
102C ALA* 1.3 79.2 - - - +
104C ASN* 1.3 57.0 + - - +
105C PRO* 3.9 4.8 - - - +
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Residues in contact with ASN 104 (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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73C LEU 4.7 0.9 - - - +
74C HIS* 3.5 23.7 + - - +
75C THR 5.2 0.2 - - - -
76C CYS 2.6 29.1 + - - +
77C ASP* 4.0 10.7 + - - +
100C VAL 2.6 12.5 + - - +
101C LYS* 3.1 9.5 - - - +
103C ALA* 1.3 72.9 - - - +
105C PRO* 1.3 61.6 - - - +
106C GLN* 3.1 20.0 + - - +
107C ALA* 2.8 41.9 + - + +
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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