Contacts of the helix formed by residues 102 - 109 (chain A) in PDB entry 2VL3
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 GLY 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.9 18.9 - - - +
99A ASP* 3.1 19.8 + - - -
100A PRO 3.4 1.0 - - - -
101A THR* 1.3 78.1 - - - +
103A ALA* 1.3 64.7 + - - +
104A PHE 3.3 2.7 - - - -
105A GLY* 3.3 4.6 + - - -
106A LYS* 3.2 28.7 + - - +
111A LEU* 4.1 9.3 - - - +
123A ARG 5.4 0.7 - - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.7 21.7 - - + +
13A GLU 5.3 1.8 - - - +
99A ASP* 2.9 13.3 + - - +
101A THR* 3.3 11.9 - - - +
102A GLY* 1.3 76.8 - - - +
104A PHE* 1.3 62.7 + - - +
106A LYS* 3.4 12.3 + - - +
107A GLU* 3.2 22.7 + - - +
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Residues in contact with PHE 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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3A ILE* 5.1 0.4 - - + -
9A ILE* 4.5 6.5 - - + -
10A PRO* 3.9 30.3 - - + -
12A VAL* 4.1 14.0 - - + +
25A LEU* 3.6 25.8 - - + -
36A LEU* 3.7 18.6 - - + -
73A LEU* 3.5 20.2 - - + -
99A ASP* 2.7 22.8 + - - +
103A ALA* 1.3 74.9 - - - +
105A GLY* 1.3 55.5 + - - +
107A GLU* 3.4 2.3 + - - +
108A THR* 2.7 46.3 + - + +
110A LEU* 3.9 13.5 - - + -
125A LEU* 4.3 10.1 - - + -
128A PHE* 3.7 23.6 - + - -
130A MET* 4.4 10.8 - - + -
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASP* 4.1 0.6 + - - -
102A GLY 3.3 5.2 + - - -
104A PHE* 1.3 79.2 - - - +
106A LYS* 1.3 53.5 + - - +
108A THR* 3.5 5.8 - - - -
109A ASP* 2.8 32.7 + - - -
110A LEU 2.9 5.9 + - - -
111A LEU* 3.6 25.7 + - - +
125A LEU* 3.8 20.1 - - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A SER* 4.1 14.7 + - - -
101A THR* 3.0 32.4 + - - -
102A GLY* 3.2 14.1 + - - +
103A ALA* 3.6 10.9 - - - +
105A GLY* 1.3 76.7 - - - +
107A GLU* 1.3 62.3 + - - +
108A THR 3.4 0.5 + - - -
109A ASP* 3.9 5.1 + - - +
111A LEU* 3.7 19.7 - - + +
123A ARG* 5.7 1.6 - - - +
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Residues in contact with GLU 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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0A SER 3.6 17.8 + - - +
1A ALA 4.5 3.5 - - - +
10A PRO* 3.6 37.1 - - + +
12A VAL* 4.8 6.6 - - + +
103A ALA 3.2 13.1 + - - +
104A PHE* 3.7 5.4 - - - +
105A GLY 3.3 0.2 - - - -
106A LYS* 1.3 78.6 - - - +
108A THR* 1.3 59.4 + - + +
109A ASP 3.6 0.2 - - - -
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Residues in contact with THR 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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1A ALA 4.5 1.6 - - - -
2A PRO* 3.4 2.2 - - - +
3A ILE* 3.0 65.9 + - + +
10A PRO* 4.1 9.9 - - + -
104A PHE* 2.7 42.7 + - + +
105A GLY* 3.3 5.5 + - - -
107A GLU* 1.3 81.6 - - + +
109A ASP* 1.3 66.8 + - - +
110A LEU* 3.3 21.6 + - - +
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Residues in contact with ASP 109 (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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0A SER 3.6 23.1 + - - +
2A PRO* 3.5 27.8 - - + +
105A GLY 2.8 7.8 + - - -
106A LYS 3.9 5.5 + - - -
107A GLU 3.6 1.8 - - - -
108A THR* 1.3 80.4 - - - +
110A LEU* 1.3 59.5 + - - +
111A LEU* 3.5 5.6 - - - +
123A ARG* 5.8 1.6 + - - -
126A LYS* 2.9 26.3 + - - -
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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