Contacts of the helix formed by residues 93 - 108 (chain A) in PDB entry 1VLH
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 ASP 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL 3.6 3.8 + - - -
92A THR* 1.3 68.5 - - - +
94A TYR* 1.3 64.4 + - - +
95A GLU* 3.6 14.6 - - - +
96A TYR* 3.2 38.2 + - + +
97A GLU* 3.1 23.7 + - - +
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Residues in contact with TYR 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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88A LEU* 4.8 7.9 - - + -
92A THR* 3.1 16.9 + - - +
93A ASP* 1.3 71.2 + - - +
95A GLU* 1.3 78.5 + - + +
97A GLU* 3.3 3.1 + - + +
98A LEU* 3.0 60.4 + - + +
88B LEU* 3.7 30.3 - - + +
89B ARG 2.7 30.2 + - - -
90B ALA* 5.0 6.3 - - - -
92B THR* 3.8 11.6 - - - -
94B TYR* 4.0 52.7 - + + -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 3.6 12.7 - - - +
94A TYR* 1.3 95.3 + - + +
96A TYR* 1.3 62.1 + - - +
98A LEU* 3.8 10.0 - - + +
99A GLN* 2.9 31.2 + - - +
95D GLU* 5.6 2.3 - - - +
90E ALA* 3.4 24.7 - - + +
91E VAL* 3.7 26.4 - - + +
92E THR 5.6 2.5 - - - +
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Residues in contact with TYR 96 (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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37A ASN* 3.9 13.4 + - - -
39A ARG* 4.4 25.8 - - - -
86A ARG* 4.5 8.5 - - - -
93A ASP* 3.2 38.9 + - + +
95A GLU* 1.3 79.7 - - - +
97A GLU* 1.3 66.3 + - - +
99A GLN* 3.3 20.0 + - - +
100A MET* 2.9 68.2 + - + +
200A PNS 3.6 20.9 + - - -
132E GLU* 5.3 6.1 + - - -
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Residues in contact with GLU 97 (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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86A ARG* 2.7 48.5 + - - +
87A GLY 4.7 5.2 - - - +
88A LEU* 4.6 4.5 - - + -
92A THR* 3.6 31.0 - - + +
93A ASP 3.1 5.0 + - - +
94A TYR* 3.3 9.6 + - + +
96A TYR* 1.3 84.5 - - + +
98A LEU* 1.3 60.0 + - + +
100A MET* 3.7 11.4 - - - +
101A ALA* 2.9 30.5 + - - +
115A PHE* 3.5 31.3 - - + -
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Residues in contact with LEU 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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94A TYR* 3.0 60.6 + - + +
95A GLU* 3.8 8.7 - - + +
97A GLU* 1.3 76.3 - - + +
99A GLN* 1.3 59.4 + - - +
101A ALA* 3.3 4.4 + - - +
102A LEU* 2.9 38.1 + - + +
115A PHE* 5.4 0.7 - - + -
88B LEU* 5.0 1.1 - - + +
89B ARG 4.6 1.3 - - - -
90B ALA* 4.5 14.4 - - - +
117B ILE* 3.2 42.0 - - + -
123B SER* 5.0 0.9 - - - +
124E PHE* 4.0 27.8 - - + -
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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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39A ARG* 4.7 10.9 - - - +
95A GLU 2.9 17.8 + - - +
96A TYR* 3.5 24.0 - - - +
98A LEU* 1.3 77.6 - - - +
100A MET* 1.3 58.3 + - - +
102A LEU* 3.8 1.9 - - - +
103A ALA* 2.9 28.6 + - - +
91E VAL* 4.1 15.9 - - + +
124E PHE* 3.1 38.4 - - - +
125E ILE 4.0 1.4 - - - -
126E SER* 3.1 29.5 + - - -
129E LEU* 4.1 21.9 - - + +
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Residues in contact with MET 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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72A LEU* 6.1 1.1 - - + -
86A ARG* 3.7 27.6 - - - +
96A TYR* 2.9 53.1 + - + +
97A GLU* 3.7 26.5 - - - +
99A GLN* 1.3 76.1 - - + +
101A ALA* 1.3 61.1 + - - +
103A ALA* 3.9 4.7 - - - +
104A ASN* 2.9 45.1 + - - +
200A PNS 3.9 43.3 - - + +
129E LEU* 5.3 1.8 - - + -
132E GLU* 5.8 1.6 - - - +
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Residues in contact with ALA 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 GLU 2.9 19.3 + - - +
98A LEU 3.7 3.8 - - - +
100A MET* 1.3 76.7 - - - +
102A LEU* 1.3 56.4 - - - +
104A ASN* 3.9 4.1 - - - +
105A LYS* 3.1 28.1 + - - +
111A LEU* 4.8 0.5 - - - +
113A THR* 3.9 36.4 + - + +
115A PHE* 4.4 0.9 - - + -
117B ILE* 4.0 24.7 - - + -
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Residues in contact with LEU 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 LEU* 2.9 21.4 + - + +
99A GLN* 3.8 4.0 - - - +
101A ALA* 1.3 74.1 - - - +
103A ALA* 1.3 59.1 + - - +
105A LYS* 3.4 11.3 + - + +
106A LYS* 3.0 31.1 + - - +
117B ILE* 4.2 16.8 - - + +
118B ALA 3.8 20.9 - - - +
119B SER* 4.2 5.2 - - - -
120B GLU* 3.6 33.7 - - + +
123B SER* 5.5 0.4 - - - +
124E PHE* 3.5 47.6 - - + -
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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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99A GLN 2.9 18.2 + - - +
100A MET 3.9 3.1 - - - +
102A LEU* 1.3 73.4 - - - +
104A ASN* 1.3 65.1 + - - +
106A LYS* 3.0 7.4 + - - +
107A LEU* 2.9 27.6 + - - +
200A PNS 4.0 7.9 - - - -
129E LEU* 3.7 29.4 - - + -
143E TRP* 3.9 23.7 - - + -
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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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71A LEU* 6.0 0.2 - - - +
72A LEU* 4.0 13.8 - - - +
73A VAL* 3.7 18.2 - - + +
84A LEU* 3.8 18.6 - - - +
100A MET* 2.9 37.4 + - - +
101A ALA* 3.9 4.3 - - - +
103A ALA* 1.3 77.0 - - - +
105A LYS* 1.3 56.3 + - - +
107A LEU* 3.2 6.7 + - - +
108A TYR* 2.8 33.3 + - - +
111A LEU* 3.4 20.4 - - + -
113A THR* 5.0 0.4 + - - -
200A PNS 3.3 28.9 - - - +
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Residues in contact with LYS 105 (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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101A ALA 3.1 18.6 + - - +
102A LEU* 3.8 12.1 - - + +
103A ALA 3.2 0.2 - - - -
104A ASN* 1.3 73.4 - - - +
106A LYS* 1.3 65.8 + - - +
108A TYR 3.2 22.1 - - - +
109A SER* 2.6 40.2 + - - +
110A ASP 4.1 1.2 - - - -
111A LEU* 2.6 33.3 + - + +
112A GLU* 3.2 20.9 + - - +
22B ARG* 4.0 24.2 - - - +
119B SER* 6.3 3.8 - - - -
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Residues in contact with LYS 106 (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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102A LEU 3.0 16.2 + - - +
103A ALA* 3.2 9.9 - - - +
105A LYS* 1.3 79.3 - - - +
107A LEU* 1.3 61.7 + - + +
108A TYR* 4.5 0.2 - - - -
109A SER* 4.5 4.2 + - - -
120B GLU* 3.2 34.1 + - - +
121E LYS 6.1 0.9 - - - -
142E GLU* 3.0 41.1 - - + +
143E TRP* 4.0 27.1 - - + +
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Residues in contact with LEU 107 (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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71A LEU* 4.6 9.9 - - + -
73A VAL* 3.8 20.9 - - + -
77A LYS* 2.8 23.6 + - - -
103A ALA 2.9 23.8 + - - +
104A ASN* 3.2 17.0 + - - +
106A LYS* 1.3 76.0 - - + +
108A TYR* 1.3 58.0 + - - +
109A SER 4.1 0.4 - - - -
200A PNS 4.9 0.4 - - - -
133E VAL* 4.0 30.7 - - + -
138E GLY* 4.8 2.0 - - - -
139E ASP* 3.3 41.5 - - + +
143E TRP* 4.3 8.5 - - + -
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Residues in contact with TYR 108 (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 VAL* 3.8 16.6 - - + -
76A LEU* 3.8 16.4 + - + -
77A LYS* 3.5 38.0 - - + +
80A GLY* 4.5 1.7 - - - -
81A ILE 2.8 30.2 + - - -
82A LYS* 3.6 21.1 - - - +
104A ASN 2.8 12.4 + - - +
105A LYS* 3.2 6.5 - - - +
107A LEU* 1.3 80.3 - - - +
109A SER* 1.3 61.6 + - - +
110A ASP* 4.0 24.5 - - + -
111A LEU* 3.0 50.2 + - + +
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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