Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 4F8Q
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 GLY 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER* 5.2 7.6 - - - -
91A ASP 3.3 1.7 + - - -
92A SER* 1.3 75.7 + - - +
94A LYS* 1.3 70.1 + - - -
95A TYR* 3.6 9.6 - - - -
111A GLU* 3.7 4.0 - - - -
112A LEU 2.9 33.4 + - - -
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Residues in contact with LYS 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 SER* 3.7 2.6 - - - -
41A SER* 2.7 38.5 + - - +
42A SER* 3.8 18.5 + - - +
93A GLY* 1.3 77.6 - - - -
95A TYR* 1.3 59.0 + - - +
109A LEU* 3.6 29.6 - - + -
110A VAL 3.5 5.4 - - - +
111A GLU* 4.4 25.1 + - + +
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Residues in contact with TYR 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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21A LEU* 3.7 27.4 - - + -
38A TRP* 4.6 9.4 - + + -
39A VAL 3.4 7.0 - - - +
40A SER* 3.7 17.3 - - - -
41A SER 3.8 0.2 - - - +
47A VAL* 3.8 21.1 - - + -
64A TYR* 3.0 36.4 + + - -
82A LEU* 4.8 4.7 - - + -
84A ILE* 3.9 11.6 - - + +
91A ASP* 2.6 35.2 + - - +
93A GLY* 3.6 15.9 - - - -
94A LYS* 1.3 76.1 - - - +
96A LEU* 1.3 64.1 + - - +
97A CYS 4.2 0.2 + - - -
109A LEU* 3.3 6.7 - - - +
110A VAL* 2.8 41.0 + - + +
112A LEU* 4.0 11.4 - - + -
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Residues in contact with LEU 96 (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 LYS 3.5 1.4 - - - +
38A TRP* 3.3 6.8 - - - -
39A VAL* 2.8 45.7 + - + -
41A SER* 4.0 11.7 - - - +
44A ARG* 3.4 39.9 - - - +
95A TYR* 1.3 73.2 - - - +
97A CYS* 1.3 60.0 + - - +
98A TYR* 3.7 21.6 - - + +
107A LYS* 4.5 16.8 - - + +
108A ALA 3.3 13.9 - - - +
109A LEU* 3.8 26.0 - - + -
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Residues in contact with CYS 97 (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 VAL* 3.7 5.3 - - - +
23A CYS* 2.0 52.5 - - + -
37A LYS 3.4 4.3 - - - -
38A TRP* 3.4 25.8 - - + +
95A TYR 4.2 0.4 + - - -
96A LEU* 1.3 72.6 - - - +
98A TYR* 1.3 60.5 + - - +
99A PHE* 5.2 1.1 - - + -
106A GLU 3.9 0.2 - - - +
107A LYS* 3.1 5.4 - - - -
108A ALA* 2.9 43.9 + - - -
110A VAL* 4.9 0.7 - - + -
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Residues in contact with TYR 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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35A GLU 4.4 0.9 - - - +
36A LEU* 3.4 6.8 - - - +
37A LYS* 2.8 72.1 + - + +
38A TRP* 5.5 1.2 - - - -
39A VAL* 3.8 20.0 - - + +
44A ARG* 4.1 9.4 + - - -
96A LEU* 3.7 37.6 - - + +
97A CYS* 1.3 77.9 - - - +
99A PHE* 1.3 71.4 + - - +
100A GLN* 4.2 2.2 - - + -
105A TYR* 3.9 34.1 - + + -
106A GLU 3.3 4.7 - - - +
107A LYS* 3.8 28.7 + - + +
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Residues in contact with PHE 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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2A PHE* 3.6 14.7 - - + -
4A VAL* 3.8 18.6 - - + -
23A CYS* 3.9 29.6 - - + -
25A LEU* 3.5 26.0 - - + -
31A ALA* 3.6 25.8 - - + -
34A MET* 4.2 4.3 - - - -
35A GLU 3.5 4.5 - - - -
36A LEU* 3.4 23.1 - - + -
38A TRP* 5.3 3.4 - + - -
75A ILE* 4.4 3.4 - - + -
78A GLY 3.8 20.9 - - - -
80A ALA* 3.9 21.3 - - + -
97A CYS* 5.0 2.2 - - + -
98A TYR* 1.3 80.2 - - - +
100A GLN* 1.3 61.2 + - - +
105A TYR* 3.3 3.6 - - - -
106A GLU 3.1 29.1 + - - -
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Residues in contact with GLN 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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33A THR 4.9 0.3 - - - +
34A MET* 3.6 7.1 - - - +
35A GLU* 2.9 63.0 + - + +
37A LYS* 5.2 7.4 + - - -
98A TYR* 5.7 3.1 - - + -
99A PHE* 1.3 74.7 - - - +
101A ASP* 1.3 59.5 + - - +
102A GLY* 3.1 28.7 + - - +
103A ASP* 5.3 1.3 - - - +
104A PHE 3.3 12.1 - - - +
105A TYR* 3.8 22.4 - - + +
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Residues in contact with ASP 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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0A LEU* 3.1 46.7 + - - +
2A PHE* 4.3 5.6 - - + -
33A THR* 4.6 12.5 + - - +
34A MET* 3.8 31.4 - - + +
99A PHE 4.2 0.8 - - - -
100A GLN* 1.3 71.4 - - - +
102A GLY* 1.3 66.6 + - - +
103A ASP 3.3 0.3 + - - -
104A PHE* 2.8 26.1 + - - +
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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