Contacts of the helix formed by residues 86 - 104 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 4.5 5.5 - - - +
84A LEU* 3.5 9.3 - - - +
85A GLY* 1.3 78.5 - - - +
87A ALA* 1.3 64.3 + - - +
88A GLU* 3.6 11.4 + - - +
89A GLN* 3.0 28.2 + - - +
90A GLY* 3.2 16.3 + - - -
125A ALA* 5.5 1.1 - - - -
126A PRO 5.8 1.6 - - - -
128A VAL* 4.1 10.1 - - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 1.3 71.5 - - - +
88A GLU* 1.3 65.5 + - - +
90A GLY* 3.2 2.9 + - - +
91A GLU* 2.9 23.8 + - - +
126A PRO 5.4 1.0 + - - -
127A GLY* 3.7 31.8 - - - +
128A VAL* 4.4 3.8 - - - +
131A PHE* 4.0 21.9 - - + -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 3.6 22.4 - - + +
86A SER* 3.1 9.8 + - - +
87A ALA* 1.3 80.5 - - - +
89A GLN* 1.3 62.0 + - - +
91A GLU* 3.3 5.4 + - - +
92A HIS* 3.0 49.0 + - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.9 32.1 + - - +
39A VAL* 5.7 1.6 - - - +
54A VAL* 5.3 6.7 - - - +
55A MSE 5.0 6.3 + - - -
57A PRO* 4.2 16.0 - - + +
60A LEU* 4.1 18.5 - - + +
83A TYR 4.0 3.6 - - - +
84A LEU* 3.2 21.2 - - + +
85A GLY* 2.9 31.2 + - - +
86A SER* 3.0 25.4 + - - +
88A GLU* 1.3 74.4 - - - +
90A GLY* 1.3 66.3 + - - +
92A HIS* 3.1 14.4 + - - +
93A ILE* 3.1 16.6 + - + +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 21.0 - - - +
86A SER 3.2 5.8 + - - -
87A ALA 3.2 6.1 + - - -
89A GLN* 1.3 79.3 - - - +
91A GLU* 1.3 56.1 + - - +
93A ILE* 3.0 8.6 + - - +
94A LEU* 2.8 30.3 + - - +
131A PHE* 3.6 21.4 - - - -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA 2.9 15.3 + - - +
88A GLU* 3.8 8.1 - - + +
89A GLN 3.2 0.2 - - - -
90A GLY* 1.3 75.5 - - - +
92A HIS* 1.3 60.5 + - + +
94A LEU* 3.4 10.9 + - - +
95A GLY* 3.0 23.0 + - - -
98A ARG* 3.6 23.6 + - - +
131A PHE* 3.7 15.8 - - - -
135A HIS* 3.7 30.6 + - - -
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO* 3.3 29.2 + - + +
58A SER* 3.9 22.9 - - - -
60A LEU* 4.7 6.3 - - + -
61A THR* 2.9 28.1 + - + +
88A GLU* 3.0 40.3 + - + +
89A GLN 3.1 8.5 + - - +
91A GLU* 1.3 78.1 - - + +
93A ILE* 1.3 52.8 + - - +
95A GLY* 3.1 3.4 + - - +
96A ILE* 2.8 40.2 + - - +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.0 44.4 - - + +
38A THR* 5.5 0.7 - - + -
60A LEU* 4.3 6.3 - - + -
79A VAL* 4.4 9.6 - - + -
81A SER* 4.0 26.9 - - - -
84A LEU* 3.6 31.6 - - + -
89A GLN* 3.1 12.9 + - + +
90A GLY* 3.0 9.5 + - - +
92A HIS* 1.3 74.5 - - - +
94A LEU* 1.3 59.9 + - + +
96A ILE* 3.0 10.1 + - + +
97A VAL* 2.8 29.6 + - + +
109A TYR* 4.3 11.4 - - + +
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Residues in contact with LEU 94 (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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90A GLY 2.8 17.9 + - - +
91A GLU* 3.4 9.8 + - - +
92A HIS 3.3 0.2 - - - -
93A ILE* 1.3 77.3 - - + +
95A GLY* 1.3 62.4 + - - +
97A VAL* 3.7 5.9 - - + +
98A ARG* 3.1 45.4 + - - +
109A TYR* 3.5 37.5 - - + +
131A PHE* 3.4 33.2 - - + -
135A HIS* 3.6 28.3 - - + +
136A GLY* 4.6 1.1 - - - -
139A ALA* 3.9 14.4 - - + -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU 3.0 13.5 + - - -
92A HIS* 3.1 6.0 + - - -
94A LEU* 1.3 78.0 - - - +
96A ILE* 1.3 61.1 + - - +
98A ARG* 3.5 22.4 + - - +
99A GLN* 3.1 24.7 + - - +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 20.2 - - + -
8A ILE* 4.1 20.6 - - + -
36A LEU* 4.3 0.2 - - + -
60A LEU* 3.9 31.9 - - + -
61A THR* 4.1 8.7 - - + +
64A VAL* 3.6 42.2 - - + -
65A GLN* 5.8 0.2 - - - +
79A VAL* 4.6 3.1 - - + -
92A HIS 2.8 21.4 + - - +
93A ILE* 3.3 9.2 - - + +
95A GLY* 1.3 77.1 - - - +
97A VAL* 1.3 55.7 + - - +
99A GLN* 3.2 9.8 + - - +
100A VAL* 2.8 31.3 + - + +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.8 33.9 - - + -
93A ILE 2.8 25.1 + - - +
94A LEU* 3.7 10.3 - - + +
95A GLY 3.4 0.2 - - - -
96A ILE* 1.3 70.9 - - - +
98A ARG* 1.3 60.0 - - + +
100A VAL* 3.2 2.3 + - - +
101A LYS* 2.8 48.3 + - + +
108A LYS 6.0 0.2 - - - -
109A TYR* 3.8 41.7 - - + -
139A ALA* 4.9 7.0 - - + +
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Residues in contact with ARG 98 (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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91A GLU* 3.6 25.7 + - - +
94A LEU* 3.1 31.4 + - - +
95A GLY* 3.5 23.8 - - - +
97A VAL* 1.3 81.3 - - + +
99A GLN* 1.3 59.5 + - - +
101A LYS* 3.8 6.0 - - - +
102A ALA* 3.0 29.3 + - - +
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Residues in contact with GLN 99 (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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64A VAL* 3.7 11.6 - - + +
65A GLN* 2.5 47.2 + - - -
68A ALA* 4.0 18.6 - - - +
73A LEU* 3.5 12.9 - - + +
95A GLY 3.1 13.0 + - - +
96A ILE* 3.2 10.4 + - - +
98A ARG* 1.3 79.9 - - - +
100A VAL* 1.3 61.0 + - - +
102A ALA* 3.4 7.8 + - - +
103A ALA* 3.3 20.4 + - - +
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Residues in contact with VAL 100 (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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6A LEU* 4.6 2.5 - - + -
73A LEU* 3.9 31.4 - - + +
76A CYS* 3.7 29.2 - - + +
79A VAL* 3.8 21.3 - - + -
96A ILE* 2.8 29.8 + - + +
97A VAL 3.2 4.2 + - - +
99A GLN* 1.3 71.4 - - - +
101A LYS* 1.3 54.3 + - + +
103A ALA* 3.1 4.7 + - - +
104A ASN* 2.7 32.9 + - - +
107A ALA* 3.5 24.5 - - + -
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Residues in contact with LYS 101 (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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97A VAL* 2.8 37.2 + - + +
98A ARG* 3.9 6.3 - - - +
100A VAL* 1.3 76.0 - - + +
102A ALA* 1.3 63.1 + - - +
104A ASN 3.3 7.6 - - - +
105A PRO* 3.0 33.8 - - + +
107A ALA* 3.3 26.9 + - + +
108A LYS 4.6 0.4 - - - -
109A TYR 4.4 3.1 - - - +
139A ALA 4.0 11.1 + - - -
141A ASP* 2.6 38.4 + - - -
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Residues in contact with ALA 102 (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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98A ARG 3.0 18.5 + - - +
99A GLN* 3.7 7.4 - - - +
100A VAL 3.2 0.4 - - - -
101A LYS* 1.3 79.0 - - - +
103A ALA* 1.3 58.6 + - - +
104A ASN 3.7 0.2 + - - -
105A PRO* 4.5 7.7 - - - +
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Residues in contact with ALA 103 (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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73A LEU* 4.0 13.5 - - + -
74A HIS* 3.4 40.0 - - + +
99A GLN 3.3 9.3 + - - +
100A VAL 3.1 8.4 + - - +
102A ALA* 1.3 77.8 - - - +
104A ASN* 1.3 58.4 + - - +
105A PRO* 4.1 3.7 - - - +
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Residues in contact with ASN 104 (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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73A LEU 4.8 0.2 - - - +
74A HIS* 3.4 23.3 + - - +
76A CYS 2.8 30.5 + - - +
77A ASP* 3.9 12.7 + - - +
100A VAL 2.7 13.3 + - - +
101A LYS* 3.1 15.9 - - - +
103A ALA* 1.3 74.8 - - - +
105A PRO* 1.3 62.4 - - - +
106A GLN* 3.1 21.3 + - - +
107A ALA* 3.0 26.9 + - - +
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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
------------------------------------------------------------
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