Contacts of the helix formed by residues 130 - 136 (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 ASN 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 6.2 0.2 - - - +
123A LEU* 3.4 45.0 - - + +
124A THR* 3.3 17.2 - - - +
127A SER* 2.9 20.4 + - - +
129A VAL* 1.3 80.9 - - - +
131A PHE* 1.3 84.5 + - - +
132A SER* 2.7 31.5 + - - -
133A GLY 3.2 3.5 + - - -
134A VAL* 3.2 13.9 + - - +
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Residues in contact with PHE 131 (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* 4.0 10.5 - - + -
99A MET* 3.6 61.2 - - + -
102A TYR* 3.7 32.3 - + + -
124A THR* 4.1 14.6 - - + -
130A ASN* 1.3 99.2 - - - +
132A SER* 1.3 58.8 + - - +
134A VAL* 4.4 6.5 - - - -
135A GLN* 2.8 40.9 + - + +
136A TYR* 4.8 7.2 - + - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 3.9 7.6 - - - -
123A LEU 3.2 4.5 + - - -
124A THR 3.3 19.7 - - - -
126A GLY* 2.9 25.7 + - - -
127A SER 3.5 0.9 + - - -
130A ASN* 2.7 22.8 + - - -
131A PHE* 1.3 85.9 - - - +
133A GLY* 1.3 59.0 + - - +
136A TYR* 3.1 28.2 + - - -
138A PHE* 3.3 24.4 - - - -
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY* 3.6 16.1 - - - -
127A SER 3.2 17.1 + - - -
128A PRO* 4.3 6.8 - - - +
130A ASN 3.2 3.8 + - - -
132A SER* 1.3 81.3 + - - +
134A VAL* 1.3 61.7 + - - +
135A GLN 3.5 0.2 - - - -
136A TYR 3.1 15.9 - - - +
138A PHE* 4.4 2.7 - - - -
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Residues in contact with VAL 134 (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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108A HIS* 4.5 8.3 + - - -
128A PRO 3.4 21.8 - - - +
129A VAL 4.8 2.0 - - - -
130A ASN 3.2 20.9 + - - +
131A PHE* 3.9 5.8 - - - +
133A GLY* 1.3 77.9 - - - +
135A GLN* 1.3 63.9 + - + +
136A TYR 4.6 0.4 - - - -
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Residues in contact with GLN 135 (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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108A HIS* 3.4 44.5 + - - +
109A GLY* 2.9 24.3 + - - -
131A PHE* 2.8 23.2 + - + +
134A VAL* 1.3 82.5 - - + +
136A TYR* 1.3 90.1 + - + +
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Residues in contact with TYR 136 (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 4.9 0.5 + - - -
102A TYR* 3.5 47.4 + + + +
103A PHE* 3.7 9.9 + - - +
106A LEU* 3.5 33.9 + - + -
107A GLU 3.5 23.3 - - - -
108A HIS 4.4 0.2 - - - -
109A GLY* 4.3 4.0 - - - +
110A ASP 3.5 11.4 - - - +
112A VAL* 4.0 4.5 - - + -
131A PHE* 4.8 5.3 - + - -
132A SER* 3.1 27.3 + - - +
133A GLY 3.1 20.6 - - - +
134A VAL 4.6 0.2 - - - -
135A GLN* 1.3 112.2 + - + +
137A ASN* 1.3 61.4 + - - +
138A PHE* 3.3 20.2 + + + -
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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