Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 2VMX
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 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 PRO* 3.1 2.5 + - - +
92A HIS* 1.3 80.3 - - - +
94A GLY* 1.3 59.1 + - - +
95A ALA* 3.3 6.4 + - - +
96A GLN* 2.7 35.1 + - - +
97A ALA 3.0 22.9 + - - -
232A ARG* 6.4 0.9 - - - -
233A GLY* 3.7 4.0 - - - -
234A GLY* 3.5 20.6 - - - +
501A PLP 3.5 17.3 - - - -
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Residues in contact with GLY 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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93A SER* 1.3 67.9 - - - +
95A ALA* 1.3 65.9 + - - +
97A ALA* 3.3 7.2 + - - +
98A ASN* 3.0 29.5 + - - -
222A THR 4.5 4.7 - - - -
223A THR* 3.4 19.3 - - - +
234A GLY* 4.1 0.2 - - - -
501A PLP 3.0 33.9 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 3.3 6.7 - - - +
94A GLY* 1.3 76.4 - - - +
96A GLN* 1.3 70.0 + - - +
98A ASN* 3.4 2.8 + - - +
99A MET* 2.9 27.9 + - - +
124A THR* 4.2 22.7 - - + -
131A PHE* 4.0 9.4 - - + -
501A PLP 2.9 19.7 + - - +
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Residues in contact with GLN 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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91A PRO* 4.4 2.2 - - + -
92A HIS* 4.1 14.8 - - + +
93A SER* 2.7 33.8 + - - +
95A ALA* 1.3 82.3 - - - +
97A ALA* 1.3 60.5 + - - +
99A MET* 3.6 31.1 - - - +
100A ALA* 2.9 26.9 + - - +
250A ILE* 4.2 0.6 - - - +
254A ILE* 3.2 20.6 - - + +
255A GLN* 3.3 30.5 - - + +
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Residues in contact with ALA 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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91A PRO* 3.8 17.1 - - + +
93A SER 3.0 16.9 + - - +
94A GLY* 3.6 5.6 - - - +
96A GLN* 1.3 75.8 - - - +
98A ASN* 1.3 62.7 + - - +
100A ALA 3.4 0.3 + - - -
101A VAL* 3.2 25.6 + - - +
221A THR* 4.0 9.9 - - - -
222A THR 4.2 5.2 - - - +
235A MET 3.8 26.0 - - - +
236A ILE* 3.6 13.5 - - + +
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Residues in contact with ASN 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 GLY 3.0 18.3 + - - +
95A ALA 3.7 3.6 - - - +
97A ALA* 1.3 72.5 - - - +
99A MET* 1.3 65.1 + - - +
101A VAL* 3.2 3.5 + - - +
102A TYR* 3.0 37.4 + - + -
124A THR* 2.8 30.6 + - - +
125A HIS* 3.8 5.3 + - - -
131A PHE* 4.9 0.2 - - + -
195A MET* 3.4 13.9 - - + +
197A ASP* 3.0 20.9 + - - +
221A THR* 2.7 34.7 + - - +
501A PLP 4.0 3.6 - - - -
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Residues in contact with MET 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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95A ALA* 2.9 18.4 + - + +
96A GLN* 3.6 31.0 - - - +
98A ASN* 1.3 73.0 - - - +
100A ALA* 1.3 57.4 + - - +
102A TYR* 3.4 3.0 + - - +
103A PHE* 2.9 30.5 + - + +
131A PHE* 3.6 53.7 - - + -
136A TYR* 4.9 0.3 + - - -
254A ILE* 3.9 30.5 - - + +
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Residues in contact with ALA 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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96A GLN 2.9 17.2 + - - +
97A ALA 3.7 4.3 - - - +
98A ASN 3.2 0.4 - - - -
99A MET* 1.3 72.5 - - - +
101A VAL* 1.3 56.3 + - - +
103A PHE* 3.4 6.1 + - - +
104A THR* 2.7 37.4 + - - -
236A ILE* 3.8 8.7 - - + -
246A ILE* 5.0 1.3 - - + +
249A ALA* 3.4 12.4 - - + +
250A ILE* 3.5 29.6 - - + -
254A ILE* 3.8 10.5 - - + +
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Residues in contact with VAL 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 ALA 3.2 4.9 + - - +
98A ASN 3.2 8.0 + - - +
100A ALA* 1.3 76.8 - - - +
102A TYR* 1.3 62.9 + - + +
104A THR* 3.1 16.4 + - - -
105A VAL* 3.2 17.8 + - + +
166A LEU* 5.0 1.3 - - + -
195A MET* 3.6 24.9 - - + -
219A PHE* 3.7 34.3 - - + -
221A THR* 3.5 27.8 - - + -
236A ILE* 4.0 21.1 - - + -
246A ILE* 4.1 8.5 - - + -
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Residues in contact with TYR 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 ASN* 3.0 19.6 + - + +
99A MET* 3.6 4.9 - - - +
101A VAL* 1.3 74.7 - - - +
103A PHE* 1.3 57.6 + - - +
105A VAL* 4.8 0.4 - - - -
106A LEU* 2.9 44.5 + - + +
124A THR 2.6 30.6 + - - -
125A HIS* 3.9 7.1 - - - -
131A PHE* 3.7 24.2 - + + -
132A SER* 3.9 12.1 - - - -
136A TYR* 3.5 31.8 + + + +
138A PHE* 3.7 16.9 - + - -
166A LEU* 3.6 24.0 - - + -
168A VAL* 3.9 7.8 - - + +
195A MET* 3.7 36.3 - - + +
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Residues in contact with PHE 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 MET* 2.9 18.8 + - + +
100A ALA* 3.5 6.1 - - - +
102A TYR* 1.3 76.1 - - - +
104A THR* 1.3 62.6 + - - +
106A LEU 3.9 9.8 - - - +
136A TYR* 3.7 8.9 + - - +
248A LYS 5.4 0.2 - - - -
249A ALA* 4.1 16.8 - - + -
253A GLY* 3.8 27.8 - - - -
254A ILE* 3.9 22.0 - - + -
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Residues in contact with THR 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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100A ALA 2.7 18.2 + - - -
101A VAL 3.1 9.4 + - - -
103A PHE* 1.3 79.0 - - - +
105A VAL* 1.3 72.4 + - + +
106A LEU 5.1 0.4 - - - +
219A PHE* 4.6 4.0 - - + -
242A PHE* 5.8 0.9 - - + -
245A GLN* 3.8 36.1 + - + -
246A ILE* 3.3 25.5 - - + +
249A ALA* 3.1 17.8 - - - +
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Residues in contact with VAL 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 VAL* 3.2 16.1 + - + +
104A THR* 1.3 84.1 - - + +
106A LEU* 1.3 76.1 + - + +
165A LYS* 3.2 27.7 + - - +
166A LEU* 4.5 16.2 - - + -
193A TYR* 4.1 29.8 - - + +
219A PHE* 3.4 39.9 - - + -
242A PHE* 5.5 2.2 - - + -
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Residues in contact with LEU 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 TYR* 2.9 42.9 + - + +
103A PHE* 3.9 10.2 - - - +
105A VAL* 1.3 87.1 - - + +
107A GLU* 1.3 64.6 + - - +
110A ASP* 3.4 11.2 - - + +
112A VAL* 3.6 24.9 - - + -
136A TYR* 3.5 31.1 + - + -
165A LYS* 3.8 26.2 - - + -
166A LEU* 3.8 24.7 - - + -
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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