Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 5F70
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 PHE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A SER 5.0 0.4 - - - -
35A LEU* 3.6 18.6 - - - -
87A ARG* 3.6 35.7 - - + +
88A VAL 3.2 17.3 - - - +
89A GLU* 4.3 8.5 - - + -
90A HIS 4.4 0.2 - - - +
93A TRP* 1.3 88.0 - - - +
95A ASN* 1.3 81.1 + - - +
96A ASP* 3.6 27.1 - - + -
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Residues in contact with ASN 95 (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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19A TYR* 5.0 3.5 - - + +
20A SER* 3.8 26.9 + - - +
86A CYS 3.6 1.0 - - - +
87A ARG* 3.6 0.5 - - - -
88A VAL* 2.8 41.8 + - + +
90A HIS* 4.8 2.4 + - + +
93A TRP* 3.0 32.9 - - - -
94A PHE* 1.3 78.4 - - - +
96A ASP* 1.3 61.9 + - - +
97A MET* 5.2 14.6 - - + +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A CYS* 3.5 22.2 - - - +
34A SER 4.1 6.8 - - - +
85A CYS* 3.6 17.4 - - - -
86A CYS 3.2 5.6 - - - +
87A ARG* 4.3 7.3 + - + -
94A PHE* 3.6 26.8 - - + -
95A ASN* 1.3 77.1 - - - +
97A MET* 1.3 67.1 + - - +
98A LYS 4.2 0.2 - - - -
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PRO 4.8 2.2 - - - +
17A CYS* 3.6 35.0 - - - -
18A HIS 3.7 23.3 - - - +
19A TYR* 4.1 15.3 - - + -
33A CYS* 4.1 2.9 - - - -
85A CYS* 3.5 3.3 - - - -
86A CYS* 3.0 35.8 + - + +
88A VAL* 5.6 1.3 - - + -
95A ASN* 5.2 12.3 - - + +
96A ASP* 1.3 81.5 - - - +
98A LYS* 1.3 64.7 + - - +
99A ILE* 3.7 10.1 + - + +
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Residues in contact with LYS 98 (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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2A SER* 5.5 1.6 - - - -
3A VAL* 4.1 14.6 + - - +
32A SER* 5.0 6.6 + - - +
33A CYS* 4.1 16.8 - - - +
83A VAL* 3.7 37.5 - - + +
84A TYR 3.6 4.9 - - - -
96A ASP 4.2 0.2 - - - -
97A MET* 1.3 71.1 - - - +
99A ILE* 1.3 67.9 + - - +
100A THR* 4.3 9.9 - - - +
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Residues in contact with ILE 99 (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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3A VAL* 3.6 23.8 - - + +
5A VAL* 4.2 10.5 - - + -
15A LEU* 3.7 31.0 - - + -
16A PRO* 3.2 28.9 - - + +
28A TRP* 3.7 26.5 - - + -
83A VAL* 3.6 1.7 - - - +
84A TYR* 2.8 37.8 + - + +
86A CYS* 5.1 1.6 - - + -
97A MET* 4.1 12.3 - - + +
98A LYS* 1.3 82.9 - - - +
100A THR* 1.3 74.5 + - - +
101A VAL 4.0 0.2 + - - -
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Residues in contact with THR 100 (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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3A VAL 3.0 13.4 + - - -
4A LYS* 3.3 25.4 - - + +
5A VAL* 2.8 35.2 + - - +
82A GLY 3.8 8.3 - - - +
83A VAL* 4.2 15.3 - - + +
98A LYS* 4.3 10.7 - - - +
99A ILE* 1.3 74.7 - - - +
101A VAL* 1.3 68.3 + - - +
102A SER* 5.1 2.0 - - - -
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Residues in contact with VAL 101 (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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5A VAL* 3.3 25.1 - - + +
13A VAL* 4.6 9.4 - - + -
15A LEU* 3.7 17.5 - - + -
73A ILE* 5.1 2.0 - - + -
80A ASP* 4.0 9.2 - - + +
81A SER* 3.2 3.7 - - - -
82A GLY* 2.8 36.0 + - - +
84A TYR* 3.6 30.1 - - + -
99A ILE* 4.7 0.2 - - + -
100A THR* 1.3 78.1 - - - +
102A SER* 1.3 64.5 + - - +
103A LEU* 3.6 31.0 - - + -
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Residues in contact with SER 102 (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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4A LYS* 3.6 33.4 + - - -
5A VAL 3.1 7.7 + - - -
6A GLY* 3.4 4.0 - - - -
7A GLY* 2.8 32.9 + - - +
81A SER* 3.9 4.4 + - - -
100A THR* 4.3 2.4 + - - -
101A VAL* 1.3 74.7 - - - +
103A LEU* 1.3 58.1 + - - +
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Residues in contact with LEU 103 (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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6A GLY* 4.1 8.1 - - - -
7A GLY 3.3 9.9 - - - +
8A GLU 3.5 22.7 - - - +
9A ALA* 4.2 7.4 - - + -
11A PRO 5.3 0.4 - - - +
13A VAL* 4.9 7.2 - - + -
76A THR* 3.8 25.8 - - + +
77A ALA 3.6 23.3 - - - +
78A VAL* 3.6 17.3 - - - +
80A ASP* 3.7 14.8 - - + -
81A SER* 3.0 19.3 + - - +
101A VAL* 3.6 22.7 - - + -
102A SER* 1.3 83.0 + - - +
104A GLU* 1.3 61.8 + - - +
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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