Contacts of the strand formed by residues 48 - 56 (chain A) in PDB entry 5SWW
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 MET 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.4 10.3 - - - +
39A ARG* 3.1 38.6 + - - +
45A SER* 6.0 1.1 - - - +
46A VAL* 3.3 15.4 + - + +
47A LYS* 1.3 82.8 + - - +
49A ASP* 1.3 65.0 + - - +
50A GLN* 3.5 26.2 - - + +
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Residues in contact with ASP 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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36A GLU* 4.3 4.7 - - - +
37A VAL 4.0 2.7 - - - +
38A GLU* 3.4 28.3 - - - +
48A MET* 1.3 78.3 - - - +
50A GLN* 1.3 64.0 + - - +
51A HIS 4.4 0.7 - - - +
52A ARG* 3.6 41.0 + - - +
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Residues in contact with GLN 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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37A VAL* 3.1 12.9 + - + +
39A ARG* 3.0 54.5 - - + +
48A MET* 3.5 18.1 - - + +
49A ASP* 1.3 75.7 - - - +
51A HIS* 1.3 94.8 + - + +
90A TYR* 4.6 7.9 - - + -
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Residues in contact with HIS 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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35A TYR* 4.7 4.7 - - + -
36A GLU* 3.3 2.4 - - - +
37A VAL* 2.6 63.1 + - + +
49A ASP* 3.8 1.7 + - - +
50A GLN* 1.3 110.1 + - + +
52A ARG* 1.3 66.3 + - - +
81A SER 5.5 0.7 - - - -
82A LEU* 3.3 50.2 + - + +
84A LEU* 4.8 3.7 - - + +
90A TYR* 5.7 2.1 - + - -
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Residues in contact with ARG 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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12A LEU* 6.3 0.6 - - - +
35A TYR* 3.4 16.6 + - - -
36A GLU* 4.0 25.4 - - + +
49A ASP* 3.6 26.9 + - - +
51A HIS* 1.3 79.4 - - - +
53A GLY* 1.3 59.5 + - - +
164A THR* 2.9 34.4 + - - -
165A PHE* 4.0 10.0 - - + -
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TYR* 2.9 45.4 + - - -
52A ARG* 1.3 76.7 - - - +
54A PHE* 1.3 65.1 + - - +
165A PHE* 3.0 17.4 - - - -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS* 3.1 26.2 - - + -
12A LEU* 3.5 28.0 - - - -
13A MET* 3.7 31.0 - - + -
32A TYR* 4.3 18.4 - + + -
33A LEU 3.0 13.9 - - - +
34A CYS* 3.9 17.0 - - - -
35A TYR* 3.3 8.4 + - - -
53A GLY* 1.3 79.7 - - - +
55A LEU* 1.3 68.1 + - - +
56A HIS* 6.2 1.1 - + - -
165A PHE* 4.6 11.2 - + + -
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Residues in contact with LEU 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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32A TYR* 3.4 11.1 - - - -
33A LEU* 2.9 39.3 + - + +
35A TYR* 4.1 20.9 - - + -
54A PHE* 1.3 76.9 - - - +
56A HIS* 1.3 67.6 + - - +
71A ALA* 3.5 34.5 - - + +
74A ARG* 3.6 43.5 - - + +
75A PHE* 3.9 14.8 - - + -
78A LEU* 4.3 9.0 - - + -
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Residues in contact with HIS 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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30A LYS* 6.2 0.2 - - + -
31A THR 3.2 15.0 - - - +
32A TYR* 3.6 38.5 + + + +
54A PHE* 6.2 1.3 - + - -
55A LEU* 1.3 84.5 - - - +
57A ASN* 1.3 91.7 + - - +
58A GLN* 4.9 2.6 - - + +
71A ALA* 4.9 0.4 - - - -
74A ARG* 3.9 18.7 + - - +
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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