Contacts of the strand formed by residues 51 - 57 (chain G) in PDB entry 3VON
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 THR 51 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24G LYS* 5.4 6.5 - - - +
38G VAL* 4.2 17.6 - - + +
39G ILE 3.7 4.0 - - - -
40G ALA* 4.6 13.0 - - + -
49G GLY 3.9 5.3 + - - +
50G GLY* 1.3 79.0 - - - +
52G PHE* 1.3 60.8 + - - +
53G LYS* 4.1 2.1 + - - +
73G THR* 4.3 2.9 - - - +
148G ALA* 3.1 20.2 + - - +
150G ASN* 3.9 18.2 + - - +
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Residues in contact with PHE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G VAL* 3.4 5.7 - - - +
39G ILE* 2.9 45.5 + - + +
41G GLY* 4.3 2.2 - - - -
47G PHE* 3.7 33.4 - + + -
50G GLY 3.8 16.6 - - - -
51G THR* 1.3 73.3 - - - +
53G LYS* 1.3 63.4 + - - +
54G LEU* 3.3 6.0 - - + +
71G PHE* 4.0 20.4 - + + -
73G THR* 3.3 20.9 - - + +
74G LYS 4.3 3.4 - - - -
75G ILE* 3.6 36.8 - - + -
112G LEU* 4.2 12.1 - - + -
144G THR* 4.1 11.2 - - + -
148G ALA* 3.4 23.8 - - + -
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G VAL 3.6 4.5 - - - +
38G VAL* 4.7 14.8 - - + +
51G THR 4.1 2.1 + - - +
52G PHE* 1.3 72.0 - - - +
54G LEU* 1.3 66.6 + - - +
71G PHE* 3.7 2.1 - - - -
72G MET* 2.8 42.3 + - + +
73G THR* 2.5 18.2 + - - +
150G ASN* 5.6 6.5 + - - +
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Residues in contact with LEU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G HIS* 3.8 1.9 - - - -
37G VAL* 2.7 53.4 + - + +
39G ILE* 3.7 32.3 - - + +
52G PHE* 3.3 27.6 - - + +
53G LYS* 1.3 78.6 - - - +
55G GLU* 1.3 65.2 + - - +
69G VAL* 4.2 11.4 - - + -
70G ARG 3.4 10.1 - - - +
71G PHE* 3.6 31.6 - - + -
72G MET* 4.3 2.5 - - - +
105G LEU* 6.3 1.1 - - + -
108G ILE* 4.0 28.9 - - + -
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Residues in contact with GLU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ASN* 2.6 45.3 + - - +
13F PHE* 3.7 19.1 - - + -
34G TYR* 2.6 28.6 + - + +
35G PHE 3.7 4.0 - - - +
36G HIS* 5.2 4.9 - - - +
54G LEU* 1.3 73.9 - - - +
56G LEU* 1.3 60.5 + - - +
69G VAL* 3.4 8.3 - - - +
70G ARG* 2.9 38.7 + - - +
72G MET* 3.5 32.1 - - + +
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Residues in contact with LEU 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE* 4.3 2.0 - - - -
33G ARG 3.6 0.5 - - - +
34G TYR* 3.6 2.9 - - - -
35G PHE* 2.7 68.1 + - + +
37G VAL* 4.2 8.1 - - + -
54G LEU 4.2 0.2 + - - -
55G GLU* 1.3 75.6 - - - +
57G PHE* 1.3 60.6 + - - +
58G LEU* 4.0 22.7 - - + -
67G PRO* 4.3 7.6 - - + -
68G LYS 3.4 7.4 - - - +
69G VAL* 3.9 22.4 - - + -
101G ILE* 4.1 17.9 - - + -
104G VAL* 4.4 8.1 - - + -
105G LEU* 3.8 26.9 - - + -
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Residues in contact with PHE 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F VAL* 3.8 15.3 - - + -
8F LYS 3.4 26.0 - - - -
9F VAL* 4.1 22.4 - - + -
10F PRO* 3.6 21.5 - - + -
13F PHE* 3.6 29.7 - + + -
31G ASN* 4.6 0.9 - - - -
33G ARG* 3.4 21.3 - - + -
34G TYR* 4.4 1.8 - - + -
56G LEU* 1.3 75.9 - - - +
58G LEU* 1.3 74.9 + - - +
59G PRO* 3.4 30.2 - - + +
67G PRO* 3.4 4.5 - - - +
68G LYS* 2.9 41.9 + - + +
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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