Contacts of the strand formed by residues 87 - 93 (chain S) in PDB entry 3HAE
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 HIS 87 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38S TYR 3.7 0.7 - - - +
39S GLN* 3.4 1.9 - - - -
40S GLN* 2.6 53.0 + - + +
41S HIS 6.2 0.9 - - - -
42S PRO* 6.4 2.2 - - + -
86S ALA* 1.3 73.5 - - - +
88S TYR* 1.3 61.0 + - - +
89S TYR* 3.9 29.5 + - + +
103S GLY* 5.6 0.4 - - - -
104S THR 3.2 8.8 + - - +
105S ASP* 3.1 42.4 + - + -
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Residues in contact with TYR 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S GLN* 2.7 27.9 + - - -
20S ILE* 4.0 17.7 - - + -
37S TRP* 4.9 2.7 - - + -
38S TYR 3.1 4.7 - - - +
39S GLN* 2.9 50.5 + - + +
49S ILE* 3.6 26.9 - - + -
64S PHE* 4.0 8.1 - + - -
75S LEU* 3.9 15.5 - - + -
77S ILE* 4.3 7.2 - - + -
84S ASP* 2.9 37.8 + - - +
86S ALA* 3.7 13.6 - - + +
87S HIS* 1.3 75.6 - - - +
89S TYR* 1.3 55.9 + - - +
104S THR* 2.8 20.9 + - - +
106S VAL* 3.5 27.8 - - + -
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Residues in contact with TYR 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S GLN* 3.6 2.5 - - - -
37S TRP* 3.5 5.8 - - - -
38S TYR* 2.8 39.4 + - + +
40S GLN* 3.7 23.3 + - + -
87S HIS* 3.9 30.1 + + + +
88S TYR* 1.3 76.3 - - - +
90S CYS* 1.3 67.9 + - - +
100S PHE* 4.3 6.1 - - + -
101S GLY 3.6 9.6 - - - -
102S THR 4.1 1.6 - - - -
103S GLY* 3.3 33.4 - - - -
39T GLN* 3.4 10.0 + - - -
43T LYS 4.0 2.1 + - - -
44T GLY* 3.4 32.9 - - - -
45T LEU* 3.5 34.5 - - + -
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Residues in contact with CYS 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S LEU* 3.9 10.5 - - - -
6S GLN* 3.3 15.7 + - - -
22S CYS* 2.0 48.9 - - - -
35S VAL* 4.7 2.7 - - + -
36S SER 3.4 6.3 - - - +
37S TRP* 3.4 26.2 - - + -
89S TYR* 1.3 75.0 - - - +
91S TRP* 1.3 62.9 + - - +
100S PHE* 3.3 7.4 - - - -
101S GLY* 2.8 28.5 + - - -
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Residues in contact with TRP 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S LEU* 4.1 0.9 - - - -
34S TYR 4.0 8.7 - - - -
35S VAL* 3.3 6.6 - - - +
36S SER* 2.8 44.8 + - - +
38S TYR* 3.5 27.8 + + + -
90S CYS* 1.3 77.8 - - - +
92S SER* 1.3 67.6 + - - +
93S PHE 4.6 0.2 - - - -
98S TYR* 3.0 60.3 - + + +
99S VAL 3.1 14.4 - - - -
100S PHE* 3.1 42.8 - + + -
37T VAL* 5.6 0.2 - - - +
47T TRP* 5.2 2.4 - - - -
99T GLU* 4.3 1.6 - - - -
103T TYR 3.4 17.5 - - - -
105T GLY* 3.3 30.1 - - - -
106T MET* 4.6 10.3 - - + +
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Residues in contact with SER 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S LEU* 3.6 19.7 - - - -
28S ASP* 3.7 5.5 - - - -
29S VAL* 3.5 29.8 + - - -
32S TYR* 5.7 0.9 - - - +
34S TYR 3.2 11.5 + - - -
35S VAL* 4.4 5.2 - - - +
91S TRP* 1.3 83.4 - - - +
93S PHE* 1.3 71.9 + - - +
94S ALA 3.7 0.2 + - - -
98S TYR* 3.5 4.2 - - - -
99S VAL* 3.0 31.0 + - - +
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Residues in contact with PHE 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P ALA* 4.3 5.8 - - + -
4R MET 4.0 6.3 - - - -
5R TRP* 3.8 16.2 - + - -
6R ILE* 4.7 4.3 - - + -
28S ASP* 3.8 4.2 - - - +
32S TYR* 3.4 48.8 - + + +
34S TYR* 3.0 34.4 + + + -
91S TRP* 4.6 0.4 - - - -
92S SER* 1.3 82.4 + - - +
94S ALA* 1.3 63.4 + - - +
95S GLY* 3.1 44.6 - - - -
97S TYR 3.9 5.6 - - - -
98S TYR* 3.9 17.0 - + + -
103T TYR* 3.4 44.6 - + + -
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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