Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 1VIF
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 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.3 13.7 - - - -
46A TYR* 2.9 48.7 + - - -
51A THR* 3.9 7.0 - - - +
53A GLU* 1.3 73.6 - - - +
55A TYR* 1.4 66.4 + - - -
69A TYR 3.4 10.8 - - - -
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Residues in contact with TYR 55 (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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22A ALA* 3.3 11.1 - - + +
23A THR 3.1 14.6 + - - -
24A PHE* 3.3 44.1 + + + -
42A ILE* 3.7 33.2 - - + -
44A GLY 3.5 13.2 - - - -
45A TRP* 4.2 14.8 - + + +
46A TYR* 3.6 4.7 - - - -
53A GLU* 2.4 45.9 + - + +
54A GLY* 1.4 76.6 - - - -
56A ALA* 1.3 61.1 + - - +
57A VAL* 4.0 2.9 + - - +
67A GLN 3.9 0.3 - - - +
68A ILE* 3.2 4.3 - - - +
69A TYR 2.9 32.4 + - - +
71A VAL* 3.8 19.1 - - + -
74A LEU* 4.1 9.9 - - + -
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Residues in contact with ALA 56 (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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42A ILE* 3.6 5.4 - - - +
43A VAL* 2.9 29.5 + - + -
44A GLY* 3.0 28.1 + - - +
45A TRP* 4.2 2.2 - - - +
55A TYR* 1.3 74.5 - - - +
57A VAL* 1.3 60.3 + - - +
66A VAL* 3.8 19.3 - - + -
67A GLN 3.6 4.9 - - - -
68A ILE* 3.8 13.4 - - + +
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Residues in contact with VAL 57 (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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30A VAL* 3.9 13.5 - - + +
31A ARG* 6.4 0.2 - - - -
38A TRP* 3.1 32.1 + - + +
40A GLY* 3.9 23.1 - - - +
41A GLN 3.4 9.2 - - - +
42A ILE* 3.9 18.8 - - + -
55A TYR 4.2 5.2 - - - +
56A ALA* 1.3 80.6 - - - +
58A GLU* 1.3 60.4 + - - +
66A VAL* 3.4 3.9 - - - +
67A GLN 2.8 33.7 + - - +
69A TYR* 4.4 6.5 - - + -
74A LEU* 4.0 22.0 - - + -
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Residues in contact with GLU 58 (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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40A GLY* 3.2 2.3 - - - -
41A GLN* 2.9 59.0 + - - +
43A VAL* 3.9 24.9 - - + +
57A VAL* 1.3 71.6 - - - +
59A SER* 1.4 69.1 + - - +
63A PRO* 3.8 4.7 - - - +
64A GLY* 2.7 32.0 + - - +
65A SER 3.4 11.2 - - - +
66A VAL* 4.0 14.8 - - + -
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Residues in contact with SER 59 (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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38A TRP* 3.7 28.1 - - - -
39A GLN 3.5 11.0 + - - -
41A GLN* 4.0 1.7 + - - -
57A VAL 3.8 2.2 + - - -
58A GLU* 1.4 79.3 - - - +
60A GLU* 1.3 60.7 + - - +
61A ALA* 2.9 21.3 + - - +
62A HIS* 2.9 41.4 + - - +
63A PRO* 4.1 3.1 - - - +
65A SER 2.9 9.8 + - - -
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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