Contacts of the helix formed by residues 66 - 72 (chain L) in PDB entry 1VQM
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 VAL 66 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64L ILE 4.0 0.4 + - - -
65L ASP* 1.3 69.5 - - - +
67L ARG* 1.3 62.9 + - - +
69L ILE* 2.9 12.8 + - - +
70L ASP* 2.7 37.1 + - - +
108L VAL* 3.9 16.3 - - + +
109L LEU 2.9 17.1 + - - +
110L GLY* 4.0 8.7 - - - -
111L ALA 3.4 24.2 - - - +
112L GLY 4.4 4.0 - - - +
113L GLN 4.4 2.7 - - - +
114L VAL* 3.7 24.2 - - + -
118L LEU* 5.6 1.3 - - + +
120L LEU* 4.6 4.3 - - + -
129L ALA* 4.4 5.4 - - + +
132L LYS* 4.8 3.8 - - + -
133L VAL* 4.1 23.8 - - + -
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Residues in contact with ARG 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6880 A 4.0 18.7 + - - -
6980 A 5.8 1.6 + - - -
7000 A 4.1 31.4 + - - +
7450 G 3.8 33.4 + - - +
65L ASP* 3.0 31.5 + - + +
66L VAL* 1.3 83.7 - - - +
68L GLU* 1.3 70.3 + - - +
71L GLU* 2.9 39.8 + - - +
111L ALA* 2.9 29.1 + - - +
112L GLY* 3.9 7.6 - - - -
113L GLN 4.2 10.3 - - - -
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Residues in contact with GLU 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7450 G 5.6 1.1 - - - +
64L ILE* 3.4 31.8 - - + +
65L ASP 2.7 18.7 + - - +
67L ARG* 1.3 85.4 - - - +
69L ILE* 1.3 63.9 + - - +
71L GLU* 4.7 4.5 - - - +
72L ASN* 2.8 40.4 + - - +
96L VAL* 5.2 7.8 - - - +
97L VAL* 6.1 0.3 - - - -
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Residues in contact with ILE 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L ILE* 3.7 27.4 - - + -
65L ASP 4.0 2.7 - - - +
66L VAL* 2.9 15.6 + - - +
68L GLU* 1.3 77.2 - - - +
70L ASP* 1.3 62.4 + - - +
72L ASN* 3.4 12.1 + - - +
73L VAL* 3.5 14.2 + - + +
76L LEU* 4.5 11.9 - - + +
91L VAL* 4.2 17.3 - - + -
93L VAL* 4.2 24.5 - - + -
96L VAL* 5.1 7.4 - - + -
108L VAL* 4.4 6.3 - - + -
118L LEU* 4.5 9.6 - - + -
120L LEU* 3.9 38.6 - - + -
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Residues in contact with ASP 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7000 A 2.9 28.5 + - - +
66L VAL 2.7 20.6 + - - +
67L ARG 4.3 0.7 - - - +
69L ILE* 1.3 75.0 - - - +
71L GLU* 1.3 61.4 + - - +
72L ASN 3.2 1.0 + - - -
73L VAL* 3.2 27.0 - - - +
113L GLN 3.9 3.8 - - - +
114L VAL* 3.3 26.4 - - + +
115L ARG* 3.1 20.3 + - - +
116L HIS* 2.9 32.2 + - - +
118L LEU* 3.7 6.0 - - + +
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Residues in contact with GLU 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7000 A 3.1 44.0 - - + +
7450 G 2.8 46.0 + - - -
67L ARG* 2.9 26.2 + - - +
68L GLU* 4.2 6.1 - - - +
69L ILE 3.4 0.2 - - - -
70L ASP* 1.3 76.1 - - - +
72L ASN* 1.3 68.7 + - - +
73L VAL* 3.6 2.3 + - - +
74L THR* 5.5 1.4 + - - -
75L LEU* 4.8 4.5 - - - +
68O GLY* 3.6 15.8 + - - +
69O VAL* 3.9 22.3 - - + +
88O LYS* 5.7 1.7 + - - -
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Residues in contact with ASN 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLU* 2.8 36.3 + - - +
69L ILE 3.4 6.6 + - - +
70L ASP 3.1 1.0 - - - -
71L GLU* 1.3 89.9 + - - +
73L VAL* 1.3 65.1 + - - +
74L THR* 3.5 2.0 - - - -
75L LEU* 3.4 30.4 + - + +
76L LEU* 3.0 35.2 + - + +
88O LYS* 4.7 7.4 + - - -
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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