Contacts of the strand formed by residues 44 - 52 (chain F) in PDB entry 3VI4
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 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E PHE* 4.1 18.8 - - - -
105E ALA* 5.4 8.1 - - - -
106E GLY 5.6 0.2 - - - -
38F LYS 3.8 0.7 - - - +
39F GLN* 3.1 29.8 - - - +
40F ARG 3.5 5.3 + - - -
41F PRO 5.3 0.6 + - - -
42F GLY 3.7 1.8 - - - -
43F HIS* 1.3 79.6 - - - +
45F LEU* 1.3 63.1 + - - -
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 5.7 1.1 - - + -
43E GLN* 4.4 2.2 - - - +
49E PRO* 4.1 24.0 - - + -
92E PHE* 3.6 38.5 - - + -
103E PHE* 3.7 51.1 + - + +
104E GLY 5.2 1.1 + - - +
37F VAL* 4.0 13.5 - - + -
38F LYS 3.4 1.1 - - - -
39F GLN* 3.5 41.7 - - + +
43F HIS 4.4 3.3 - - - +
44F GLY* 1.3 73.5 - - - -
46F GLU* 1.3 63.0 + - - +
95F TYR* 4.9 5.2 - - + -
108F TRP* 4.7 3.4 - - + -
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PHE* 4.6 0.9 - - - -
37F VAL* 3.2 7.2 - - - +
38F LYS* 2.7 55.7 + - + +
40F ARG* 5.2 5.0 + - - +
43F HIS* 5.5 6.4 - - - +
45F LEU* 1.3 77.2 - - - +
47F TRP* 1.3 68.7 + - - +
48F LEU* 3.4 2.8 + - - +
61F ASN* 3.8 8.9 + - - +
63F LYS* 4.0 16.6 + - - +
64F PHE* 2.7 40.4 - - + -
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Residues in contact with TRP 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E TYR* 3.7 19.1 - + - -
100E PRO* 3.7 20.4 - - + -
101E PHE* 3.3 62.8 + + + +
103E PHE* 4.2 11.9 - - + -
35F GLU* 2.7 24.4 + - + +
36F TRP 3.9 11.0 - - - -
37F VAL* 4.3 7.2 - - + -
46F GLU* 1.3 73.3 - - - +
48F LEU* 1.3 57.7 + - - +
49F GLY* 3.5 26.0 + - - -
50F GLU* 3.6 15.5 - - + -
59F HIS 3.3 20.0 - - - -
60F TYR 4.0 2.5 - - - -
61F ASN* 3.1 48.2 + - + +
105F MET* 4.0 13.9 - - + -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TRP* 2.9 24.6 + - + +
37F VAL 4.5 0.2 - - - -
38F LYS* 3.7 11.7 - - + +
46F GLU 3.7 14.4 - - - +
47F TRP* 1.3 74.4 - - - +
49F GLY* 1.3 53.6 + - - +
60F TYR* 3.8 2.6 - - - -
61F ASN* 2.7 37.6 + - - +
64F PHE* 3.5 49.8 - - + +
68F ALA* 5.2 0.9 - - + -
70F PHE* 4.2 6.8 - - + -
81F MET* 2.7 41.5 - - + -
94F TYR* 4.0 21.1 - - + -
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Residues in contact with GLY 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TRP* 2.9 26.7 + - - +
47F TRP* 3.5 14.7 + - - -
48F LEU* 1.3 82.9 - - - +
50F GLU* 1.3 62.4 + - - +
59F HIS 3.0 15.5 - - - -
70F PHE* 3.8 19.2 - - - -
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLY* 4.0 3.3 - - - -
82B THR* 3.1 32.7 + - - +
99E TYR* 2.7 28.2 + - - -
33F TRP* 4.0 13.3 - - + +
34F ILE 3.1 9.9 - - - +
35F GLU* 2.4 42.6 - - - +
36F TRP* 5.1 1.1 - - - -
47F TRP* 3.6 15.7 - - + -
49F GLY* 1.3 74.9 - - - +
51F ILE* 1.3 63.9 + - - +
58F ILE* 3.4 7.9 - - - +
59F HIS* 3.0 36.6 + - + +
70F PHE* 4.6 3.1 - - - -
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Residues in contact with ILE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F TRP* 3.3 5.7 - - - -
34F ILE* 3.0 45.1 + - + +
36F TRP* 4.5 6.3 - - - +
50F GLU* 1.3 77.9 - - - +
52F LEU* 1.3 65.5 + - - +
53F PRO* 3.2 4.7 - - - +
55F SER 5.2 1.8 - - - +
56F GLY* 5.4 3.8 - - - -
57F TYR 3.5 13.5 - - - +
58F ILE* 3.6 15.3 - - + -
70F PHE* 3.7 42.8 - - + +
71F THR* 3.8 15.3 - - - +
72F THR* 3.9 24.0 - - + +
79F ALA* 5.2 0.2 - - + -
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG* 3.6 48.5 - - + +
30F THR 4.0 9.6 - - - +
32F TYR 3.8 5.8 - - - +
33F TRP* 3.2 58.4 - - + +
51F ILE* 1.3 74.8 - - - +
53F PRO* 1.3 55.6 - - + +
54F GLY* 2.7 25.5 + - - +
55F SER 2.8 27.4 + - - +
57F TYR* 3.3 21.2 + - + +
72F THR* 4.9 0.2 + - - -
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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