Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 4C48
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ILE* 5.2 0.9 - - + +
46A SER* 3.3 5.6 - - - -
47A ALA* 3.0 41.3 + - + +
57A VAL* 3.2 24.9 - - + +
61A VAL* 3.9 16.6 - - + -
62A THR* 3.2 32.5 - - + +
65A ILE* 6.2 0.2 - - + -
81A ASN* 4.0 5.8 - - - +
82A SER* 4.7 0.9 - - - +
87A THR* 1.3 75.1 - - - +
89A GLN* 1.3 68.6 + - - +
90A ILE* 3.6 32.3 - - + -
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Residues in contact with GLN 89 (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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44A THR* 3.8 27.7 - - + +
45A ILE 3.3 5.8 - - - +
46A SER* 4.8 7.4 + - - +
79A SER 4.2 0.5 - - - +
80A SER* 3.7 1.0 - - - -
81A ASN* 3.4 48.1 + - - +
88A VAL* 1.3 78.6 - - - +
90A ILE* 1.3 66.0 + - - +
91A THR* 4.5 7.4 + - - +
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Residues in contact with ILE 90 (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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44A THR* 3.5 1.8 - - - -
45A ILE* 2.8 50.4 + - + +
62A THR* 4.1 11.0 - - + +
65A ILE* 3.7 35.7 - - + -
66A GLU* 4.5 4.3 - - + +
69A MET* 5.7 0.2 - - + -
78A MET* 3.9 27.8 - - + -
79A SER 3.6 11.4 - - - +
80A SER* 3.9 14.4 - - - +
88A VAL* 3.6 22.4 - - + -
89A GLN* 1.3 78.9 - - - +
91A THR* 1.3 62.2 + - - +
92A LEU* 3.8 14.7 + - + +
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Residues in contact with THR 91 (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 ALA* 3.9 20.2 - - + -
43A VAL 3.4 15.3 - - - +
44A THR* 3.9 19.0 - - + +
77A TYR 3.9 0.7 - - - +
78A MET* 3.5 22.3 - - - -
79A SER* 3.3 24.7 + - - -
89A GLN* 4.1 8.7 + - - +
90A ILE* 1.3 75.0 - - - +
92A LEU* 1.3 59.9 + - - +
93A THR* 4.2 10.7 + - + +
132A SER 6.2 0.2 - - - +
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Residues in contact with LEU 92 (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 ALA* 3.1 3.5 - - - +
43A VAL 2.9 35.4 + - - +
45A ILE* 4.0 27.6 - - + -
69A MET* 4.4 13.9 - - + -
72A ILE* 3.5 33.2 - - + -
75A LEU* 4.7 15.9 - - + -
77A TYR 3.6 8.1 - - - +
78A MET* 4.5 10.5 - - + -
90A ILE* 4.0 13.5 - - + +
91A THR* 1.3 77.2 - - - +
93A THR* 1.3 62.1 + - - +
94A PHE* 3.3 20.4 - - + -
107A VAL* 4.0 13.9 - - + -
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Residues in contact with THR 93 (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 PRO* 4.6 10.8 - - + -
41A PRO 4.3 0.7 - - - -
42A ALA* 3.7 18.6 - - + -
75A LEU* 3.4 2.9 - - - -
76A MET* 2.5 39.6 + - - +
77A TYR* 3.0 55.0 + - + +
79A SER* 5.5 1.8 - - - +
91A THR* 4.2 13.2 - - + +
92A LEU* 1.3 79.2 - - - +
94A PHE* 1.3 56.3 + - - +
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Residues in contact with PHE 94 (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 PRO* 3.3 8.7 - - - +
41A PRO* 2.9 31.4 + - + +
42A ALA* 4.5 1.8 - - - -
43A VAL* 4.4 11.7 - - + -
72A ILE* 5.0 3.8 - - + -
73A ASP 3.3 27.6 - - - -
74A ASN* 3.3 9.9 - - + +
75A LEU* 4.2 6.1 - - + -
76A MET* 4.2 3.8 - - - -
92A LEU* 3.3 37.2 - - + -
93A THR* 1.3 81.5 - - - +
95A GLU* 1.3 67.5 + - - +
96A SER 2.9 4.5 + - - -
98A THR* 3.3 19.1 - - + -
103A ALA* 3.6 34.1 - - + -
106A GLN* 5.1 3.8 - - - -
107A VAL* 3.6 26.0 - - + -
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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