Contacts of the helix formed by residues 114 - 121 (chain K) in PDB entry 1VQ7
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 ALA 114 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49K LEU* 3.7 31.9 - - + -
74K VAL 3.6 5.5 + - - -
80K ILE* 5.3 0.4 - - + -
82K ARG* 4.6 2.0 - - - +
90K PHE* 3.7 19.7 - - + -
113K ILE* 1.3 88.3 - - - +
115K ARG* 1.3 65.0 + - - +
116K GLU* 4.0 10.8 - - - +
117K VAL* 3.2 21.3 + - + +
118K ALA* 3.9 1.9 + - - +
131K ILE* 4.5 1.4 - - - +
132K VAL* 4.1 3.4 - - - -
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Residues in contact with ARG 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 6.2 0.2 - - - +
82K ARG* 3.2 41.4 - - - +
83K PRO* 5.6 4.0 - - - +
114K ALA* 1.3 72.7 - - - +
116K GLU* 1.3 88.2 + - + +
118K ALA* 3.0 21.1 + - - +
119K GLN* 3.5 14.0 + - - +
131K ILE* 3.5 18.8 - - + -
132K VAL* 2.8 24.4 + - - +
20U MET* 5.9 1.2 - - - +
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Residues in contact with GLU 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LEU* 3.1 55.9 - - + +
5K GLY 3.9 4.6 - - - +
6K ALA* 3.5 18.9 - - + +
49K LEU* 5.9 2.0 - - + -
80K ILE* 4.2 8.1 - - + +
82K ARG* 2.8 48.7 + - - +
114K ALA* 3.2 9.1 - - + +
115K ARG* 1.3 87.4 + - + +
117K VAL* 1.3 66.1 + - + +
118K ALA 3.3 0.5 + - - -
119K GLN* 3.3 19.1 + - - +
120K ARG* 3.5 6.1 + - - +
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Residues in contact with VAL 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LEU* 4.9 3.1 - - - -
49K LEU* 3.5 31.9 - - + -
50K GLY* 4.5 4.9 - - - +
72K VAL* 3.8 17.3 - - + -
73K VAL 3.8 6.3 - - - +
74K VAL* 4.0 11.4 - - + +
113K ILE* 4.0 13.2 - - + -
114K ALA* 3.2 20.1 + - + +
116K GLU* 1.3 77.8 - - + +
118K ALA* 1.3 51.4 + - - +
120K ARG* 3.2 1.6 + - - -
121K PHE* 2.8 56.8 + - + +
124K VAL* 5.2 6.5 - - + -
125K ALA 6.0 0.2 - - - -
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Residues in contact with ALA 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ILE* 5.3 2.4 - - + +
114K ALA 3.9 2.1 + - - +
115K ARG* 3.0 16.7 + - - +
117K VAL* 1.3 76.0 - - - +
119K GLN* 1.3 67.4 + - - +
120K ARG 2.9 3.1 + - - -
121K PHE 3.5 6.1 + - - -
122K GLY* 3.7 14.2 + - - -
125K ALA* 3.4 31.1 - - + +
131K ILE* 4.7 12.6 - - + -
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Residues in contact with GLN 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K GLU* 3.6 21.8 - - - +
3K ALA 3.9 14.6 - - - +
4K LEU 3.7 22.8 + - - +
5K GLY* 4.9 5.6 + - - -
115K ARG* 3.5 13.1 + - - +
116K GLU* 3.3 17.6 + - - +
118K ALA* 1.3 78.5 - - - +
120K ARG* 1.3 60.0 + - + +
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Residues in contact with ARG 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27090 G 4.4 9.3 + - - -
27100 U 5.5 6.7 - - - -
1K MET* 3.4 37.1 - - + +
2K GLU* 2.9 37.9 + - + +
3K ALA 4.8 3.4 - - - +
4K LEU* 3.8 39.1 - - + +
49K LEU 4.9 0.2 + - - -
50K GLY 2.7 40.9 + - - -
51K ASP* 4.3 5.1 + - - -
102K GLU* 4.8 5.4 - - - +
116K GLU 3.5 3.0 + - - +
117K VAL* 3.2 3.5 + - - +
118K ALA 2.9 1.6 + - - -
119K GLN* 1.3 84.8 - - + +
121K PHE* 1.3 83.2 + - + +
122K GLY 3.6 4.4 + - - -
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Residues in contact with PHE 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 5.1 8.3 - - - -
50K GLY* 3.7 22.2 - - - -
52K LYS* 4.6 15.9 - - + -
72K VAL* 3.3 49.4 - - + -
102K GLU* 3.7 42.6 - - + +
117K VAL* 2.8 27.8 + - + +
118K ALA 3.7 3.1 - - - -
120K ARG* 1.3 90.9 - - + +
122K GLY* 1.3 65.2 + - - +
123K SER 3.4 2.0 - - - -
124K VAL* 3.1 23.0 + - + +
125K ALA* 2.9 20.3 + - - +
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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