Contacts of the strand formed by residues 50 - 57 (chain A) in PDB entry 4OBP
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 LEU 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.9 2.7 - - + -
41A LYS* 3.8 30.7 - - + -
42A GLY 3.4 17.0 - - - +
43A ARG* 4.6 14.6 - - + +
48A GLY 3.6 8.7 + - - +
49A GLN* 1.3 89.1 + - - +
51A ALA* 1.3 61.8 + - - +
86A TYR* 4.3 6.8 + - - -
107A PHE* 3.7 40.1 + - + +
109A GLY* 6.0 0.4 - - - -
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Residues in contact with ALA 51 (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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25A PHE* 3.8 19.3 - - + -
42A GLY* 2.6 42.3 + - - +
49A GLN 4.9 0.2 - - - +
50A LEU* 1.3 76.8 - - - +
52A ALA* 1.3 57.0 + - - +
53A ILE* 4.6 1.1 - - + -
86A TYR* 4.1 6.1 - - + -
104A VAL* 3.5 24.2 - - + -
105A MET 3.3 14.1 - - - +
107A PHE* 3.5 11.8 - - - -
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Residues in contact with ALA 52 (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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39A VAL* 4.8 4.5 - - + -
40A TYR 3.4 7.4 - - - +
51A ALA* 1.3 71.7 - - - +
53A ILE* 1.3 62.0 + - - +
54A LYS 4.2 0.2 - - - -
103A LEU 3.6 1.4 - - - +
104A VAL* 3.5 2.3 - - - -
105A MET* 2.8 43.5 + - + +
106A GLU 4.0 0.4 - - - +
107A PHE* 3.7 7.7 - - + +
403A 2QU 3.2 49.6 - - + +
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Residues in contact with ILE 53 (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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25A PHE* 3.9 31.0 - - + -
26A GLU 4.0 3.8 - - - +
27A LEU* 3.9 19.7 - - + -
39A VAL* 3.4 4.3 - - - +
40A TYR* 2.7 43.0 + - - +
42A GLY* 3.7 26.9 - - - -
51A ALA 4.3 0.9 - - - +
52A ALA* 1.3 77.9 - - - +
54A LYS* 1.3 62.3 + - - +
55A VAL* 3.7 10.3 + - + -
102A TRP* 3.8 39.5 - - + -
103A LEU 3.3 6.1 - - - +
104A VAL* 3.9 15.5 - - + -
105A MET* 5.1 0.2 - - - -
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Residues in contact with LYS 54 (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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36A TYR 4.8 6.3 + - - -
38A GLN 3.7 4.3 - - - +
39A VAL* 3.8 17.7 - - + -
52A ALA 4.2 0.4 - - - -
53A ILE* 1.3 69.1 - - - +
55A VAL* 1.3 63.2 + - - +
56A MET* 3.9 18.8 + - + +
69A GLU* 2.7 41.7 + - - +
101A LEU 3.4 4.3 - - - +
102A TRP* 3.5 0.2 - - - -
103A LEU* 2.8 51.9 + - + +
105A MET* 4.1 10.4 - - + +
171A ASP* 3.1 13.9 + - - -
173A GLY* 4.3 2.4 - - - -
403A 2QU 3.1 33.2 + - + +
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Residues in contact with VAL 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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27A LEU* 4.1 7.9 - - + -
38A GLN* 2.8 46.4 + - + +
40A TYR* 3.6 31.2 - - + +
53A ILE* 4.0 11.2 - - + -
54A LYS* 1.3 74.6 - - - +
56A MET* 1.3 62.8 + - - +
57A ASP* 5.4 2.6 - - - +
100A GLN* 3.5 38.8 - - + +
101A LEU 3.3 2.9 - - - -
102A TRP* 3.9 22.0 - - + +
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Residues in contact with MET 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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54A LYS* 4.3 26.7 - - + +
55A VAL* 1.3 79.3 - - - +
57A ASP* 1.3 61.6 + - - +
65A GLU 5.1 0.9 - - - +
66A ILE* 3.7 42.0 - - + +
69A GLU* 3.2 41.1 - - + +
100A GLN* 3.6 1.3 - - - -
101A LEU* 2.7 63.5 + - + +
103A LEU* 4.7 9.2 - - - -
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Residues in contact with ASP 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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38A GLN* 5.8 3.1 + - - +
55A VAL* 5.4 2.3 - - - +
56A MET* 1.3 74.6 - - - +
58A VAL* 1.4 59.3 + - - +
59A THR* 3.0 29.1 + - + -
62A GLU* 4.0 8.0 - - - +
66A ILE* 4.2 6.9 - - - +
98A ASP* 3.8 23.3 - - + +
99A ASP 3.6 7.1 - - - +
100A GLN* 3.6 25.1 + - - +
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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