Contacts of the strand formed by residues 56 - 62 (chain A) in PDB entry 6D4A
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.3 7.6 - - + -
45A HIS* 4.1 5.6 - - + -
54A SER 4.5 0.2 - - - +
55A PRO* 1.3 72.7 - - - +
57A HIS* 1.3 73.3 + - - +
76A ASN* 3.4 16.5 + - - -
96A PRO* 3.4 35.2 - - + +
97A SER* 4.1 20.8 + - - -
120A MET* 4.2 15.5 - - + -
121A GLU 3.5 6.7 - - - +
122A ARG* 3.3 43.3 - - + +
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Residues in contact with HIS 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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55A PRO* 4.1 29.6 + - + +
56A VAL* 1.3 84.1 - - - +
58A GLY* 1.3 59.8 + - - +
59A TYR* 3.4 31.2 + - + +
76A ASN* 3.2 14.8 - - - +
77A LYS* 3.9 42.4 + - + +
120A MET* 3.3 7.8 - - - +
121A GLU* 2.8 40.8 + - - +
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Residues in contact with GLY 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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57A HIS* 1.3 72.6 - - - +
59A TYR* 1.3 58.5 + - - -
75A THR* 2.8 33.8 + - - -
76A ASN* 2.7 15.5 + - - -
92A LEU* 3.6 13.2 - - - -
96A PRO* 3.8 5.7 - - - +
118A PHE* 3.6 17.9 - - - -
119A ARG 3.5 6.7 - - - -
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Residues in contact with TYR 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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57A HIS* 3.4 28.5 + - + +
58A GLY* 1.3 72.5 - - - -
60A TRP* 1.3 60.7 + - - +
61A PHE* 3.4 27.8 + + + -
72A PRO* 4.0 14.4 - - + -
74A ALA 3.3 7.0 - - - -
75A THR* 3.2 24.0 - - - -
77A LYS* 3.3 25.7 + - + +
80A GLN* 4.1 19.3 - - + -
117A PHE 3.9 0.2 - - - +
118A PHE* 3.3 11.1 - - - -
119A ARG* 2.8 50.8 + - + +
121A GLU* 3.4 40.8 + - + -
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Residues in contact with TRP 60 (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 LEU* 5.4 0.4 - - + -
25A VAL* 4.3 22.0 - - + -
39A VAL* 5.9 0.2 - - + -
41A CYS* 3.8 22.7 - - + -
59A TYR* 1.3 72.4 - - - +
61A PHE* 1.3 54.3 + - - +
72A PRO* 3.2 5.0 - - - +
73A VAL* 2.7 47.2 + - + +
74A ALA* 2.8 17.4 + - + +
92A LEU* 3.7 20.4 - - + +
101A CYS 2.8 30.6 + - - -
103A LEU* 3.7 35.6 - - + +
116A TYR* 3.8 28.9 - - + -
117A PHE* 3.4 29.8 - - - -
118A PHE* 3.6 22.7 - + + -
133A GLN* 5.7 0.2 - - - -
134A LEU* 4.3 12.1 - - + -
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Residues in contact with PHE 61 (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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59A TYR* 3.4 28.3 - + + -
60A TRP* 1.3 75.9 - - - +
62A ARG* 1.3 61.5 + - - +
65A ALA* 3.8 17.7 - - + -
67A ILE* 3.5 35.7 - - + -
70A ASP 3.4 21.5 - - - -
71A SER 3.9 2.2 - - - -
72A PRO* 3.4 31.4 - - + -
73A VAL* 4.4 2.5 - - - +
116A TYR* 3.1 11.6 - - - +
117A PHE* 2.8 62.9 + + + -
119A ARG* 3.9 17.7 - - + -
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Residues in contact with ARG 62 (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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61A PHE* 1.3 74.7 - - - +
63A GLU* 1.3 77.5 + - + +
64A GLY 3.3 0.2 + - - -
65A ALA* 3.0 25.2 + - + +
71A SER 5.8 0.8 + - - -
73A VAL* 4.4 15.4 - - + +
111A ARG* 2.8 28.4 + - - +
112A ASP* 4.0 3.8 + - - +
113A ASN 2.6 30.7 + - - -
114A GLY* 4.5 2.8 - - - -
115A SER 3.7 9.6 - - - +
116A TYR* 3.6 38.0 + - + -
117A PHE* 3.7 3.5 - - - -
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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