Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 3O71
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.8 7.5 - - - -
42A ASP* 2.7 44.5 + - - +
45A ASN* 3.9 25.1 - - + +
46A LYS* 1.3 79.3 - - - +
48A ARG* 1.3 66.4 + - - +
49A VAL* 4.1 17.9 - - + -
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Residues in contact with ARG 48 (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 ASN 6.0 0.2 + - - -
27A SER* 5.4 0.8 + - - -
39A SER* 3.9 24.7 + - - -
40A ALA 3.3 10.9 + - - +
41A TYR* 4.3 16.5 - - + +
47A VAL* 1.3 85.4 - - + +
49A VAL* 1.3 63.3 + - - +
105A LEU* 3.5 42.7 + - + +
107A GLU* 4.9 11.9 + - - +
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Residues in contact with VAL 49 (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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23A TYR* 3.7 30.1 - - + -
39A SER* 3.5 4.0 - - - -
40A ALA* 2.7 49.2 + - + +
42A ASP* 4.0 21.5 - - + +
47A VAL* 4.1 11.2 - - + -
48A ARG* 1.3 77.2 - - - +
50A ALA* 1.3 57.8 + - - +
51A ILE* 4.1 8.7 - - + -
85A ASN* 5.1 6.3 - - - +
102A VAL* 4.0 16.6 - - + -
103A GLN 3.5 13.5 - - - +
104A ASP* 5.5 1.1 - - - -
105A LEU* 3.7 12.1 - - - +
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Residues in contact with ALA 50 (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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29A ILE* 5.1 2.0 - - + -
37A VAL* 4.5 13.5 - - + -
38A CYS 3.3 9.2 - - - +
49A VAL* 1.3 74.9 - - - +
51A ILE* 1.3 62.4 + - - +
101A ILE 3.7 0.5 - - - +
102A VAL* 3.4 3.3 - - - +
103A GLN* 2.8 43.7 + - + +
104A ASP 3.7 18.6 - - - +
105A LEU* 3.9 14.9 - - + +
106A MET 4.7 2.0 - - - +
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Residues in contact with ILE 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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17A PHE* 3.8 18.9 - - + -
19A VAL* 3.8 31.4 - - + -
23A TYR* 3.4 44.2 - - + -
26A LEU* 4.5 1.8 - - + -
36A MET 3.8 1.6 - - - +
37A VAL* 3.5 3.7 - - - -
38A CYS 2.9 36.7 + - - +
40A ALA* 4.0 13.7 - - + -
49A VAL* 4.1 9.4 - - + -
50A ALA* 1.3 80.5 - - - +
52A LYS* 1.3 63.1 + - - +
53A LYS 4.0 0.2 - - - -
100A TYR* 4.1 14.4 - - + -
101A ILE 3.4 7.6 - - - +
102A VAL* 4.1 11.9 - - + -
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Residues in contact with LYS 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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35A GLY* 5.8 3.8 - - - -
36A MET 3.5 11.9 - - - +
37A VAL* 4.3 18.8 - - + +
50A ALA 4.3 0.4 - - - -
51A ILE* 1.3 73.8 - - - +
53A LYS* 1.3 60.6 + - - +
54A ILE* 3.6 27.5 + - + +
69A GLU* 4.0 18.8 + - - +
99A VAL 3.3 2.4 - - - +
100A TYR* 3.3 3.5 - - - -
101A ILE* 2.8 52.0 + - + +
103A GLN* 4.7 15.3 - - - +
165A ASP* 5.5 8.3 - - - +
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Residues in contact with LYS 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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15A GLN* 4.4 10.1 - - + +
16A VAL* 2.8 42.7 + - - +
17A PHE* 3.6 23.7 - - + -
35A GLY* 3.1 25.6 - - - -
36A MET* 3.0 13.4 + - + +
51A ILE 4.0 1.4 + - - -
52A LYS* 1.3 70.3 - - - +
54A ILE* 1.3 61.9 + - - +
55A SER* 4.2 9.6 + - - +
98A ASP* 3.7 30.1 + - + -
99A VAL 3.5 3.8 - - - +
100A TYR* 3.5 33.0 - - + -
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Residues in contact with ILE 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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34A TYR* 3.6 32.8 - - + -
35A GLY* 4.6 6.5 - - - -
52A LYS* 3.6 47.6 - - + +
53A LYS* 1.3 75.2 - - - +
55A SER* 1.3 65.6 + - - +
56A PRO* 3.5 12.8 - - + +
66A THR* 3.7 19.1 - - + +
98A ASP* 3.3 4.2 - - - -
99A VAL* 2.7 51.7 + - + +
101A ILE* 4.3 14.6 - - + -
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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