Contacts of the strand formed by residues 92 - 101 (chain B) in PDB entry 5E94
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 ALA 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 4.2 13.0 - - + -
40B HIS 3.4 21.1 - - - +
41B PHE* 4.1 11.0 - - + -
42B PRO* 4.5 4.7 - - - -
90B ASP 3.2 9.6 + - - +
91B THR* 1.3 78.6 - - - +
93B THR* 1.3 63.1 + - - +
94B TYR* 3.4 16.9 - - + -
118B THR* 4.6 1.1 - - - -
119B LEU 2.8 31.3 + - - +
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Residues in contact with THR 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ARG* 3.3 2.1 - - - -
40B HIS* 2.8 45.3 + - - -
92B ALA* 1.3 72.6 - - - +
94B TYR* 1.3 62.3 + - - +
95B TYR* 3.7 34.1 - - + +
115B GLN 5.0 0.9 - - - +
116B GLY* 4.0 3.1 - - - -
117B THR 3.5 23.3 - - - +
118B THR* 3.4 21.8 - - + +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 3.6 7.7 - - - +
18B LEU* 4.1 6.7 - - + -
20B LEU* 3.4 24.7 - - + -
37B TRP* 4.6 4.3 - + + -
38B ILE 3.7 2.2 - - - -
39B ARG* 3.0 42.1 + - + -
49B MET* 3.8 15.5 - - + -
81B LEU* 3.7 22.7 - - + -
83B LEU* 3.9 3.8 - - + +
90B ASP* 2.6 34.6 + - - +
92B ALA* 3.4 21.5 - - + -
93B THR* 1.3 72.1 - - - +
95B TYR* 1.3 61.0 + - - +
116B GLY* 3.2 2.8 - - - -
117B THR* 2.8 39.2 + - + +
119B LEU* 3.7 25.8 - - + +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.3 17.5 + - - -
42A GLY* 2.5 35.1 + - - -
44A VAL* 3.8 13.0 - - + -
6B GLU* 3.2 3.8 - - - -
37B TRP* 3.4 9.9 - - - -
38B ILE* 2.7 43.5 + - + +
40B HIS* 4.1 17.5 - - + -
46B LEU* 5.0 4.5 - - + -
93B THR* 3.7 34.9 - - + +
94B TYR* 1.3 73.2 - - - +
96B CYS* 1.3 59.9 + - - +
113B TRP* 3.9 32.8 - + + -
114B GLY 3.5 12.6 - - - -
115B GLN 3.4 16.7 + - - -
116B GLY* 3.4 13.0 - - - -
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Residues in contact with CYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 11.7 - - - -
5B GLN 4.3 2.0 - - - -
6B GLU* 2.8 29.4 + - - +
22B CYS* 2.1 53.2 - - + -
36B HIS 3.2 11.7 - - - +
37B TRP* 4.0 9.2 - - + -
79B PHE* 3.7 5.6 - - + -
95B TYR* 1.3 75.7 - - - +
97B ALA* 1.3 62.9 + - - +
113B TRP* 3.6 2.3 - - - +
114B GLY 2.9 26.3 + - - -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 7.8 - - - +
35B TRP* 3.6 3.1 - - - -
36B HIS* 2.8 35.2 + - + +
38B ILE* 4.2 17.7 - - + -
79B PHE* 4.5 0.3 - - - -
96B CYS* 1.3 76.2 - - - +
98B ARG* 1.3 60.0 + - - +
110B PHE* 4.2 19.5 - - + -
112B TYR 3.2 12.1 - - - +
113B TRP* 4.2 18.4 - - + -
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.4 25.2 - - - +
4B LEU* 3.9 4.0 - - + +
27B TYR* 4.0 11.7 - - - -
33B TYR* 3.4 58.8 + - + -
34B ASP 3.6 3.6 - - - +
35B TRP* 3.4 37.0 - - + -
97B ALA* 1.3 72.3 - - - +
99B ALA* 1.3 63.0 + - - +
100B THR* 4.8 0.2 - - - -
110B PHE* 3.2 8.6 - - - -
111B ASP* 2.7 60.5 + - - +
112B TYR* 2.8 34.9 + - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 3.4 25.4 - - - +
34B ASP* 2.9 14.4 + - + +
36B HIS* 3.4 16.8 - - + +
97B ALA 4.0 0.8 + - - -
98B ARG* 1.3 72.4 - - - +
100B THR* 1.3 59.9 + - - +
108B TYR* 3.4 40.2 - - + +
109B TYR 3.3 9.0 - - - +
110B PHE* 3.8 5.8 - - + -
32G LEU* 3.6 2.9 - - - +
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 3.2 26.8 - - - -
98B ARG* 4.1 1.4 + - - -
99B ALA* 1.3 75.4 - - - +
101B ALA* 1.3 76.8 + - - +
108B TYR* 3.4 5.9 - - - -
109B TYR* 2.9 65.0 + - + +
111B ASP* 3.4 23.1 - - - +
32G LEU* 3.7 8.5 - - - -
141G LEU* 3.7 8.7 - - - +
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 1.3 86.9 + - - +
102B SER* 1.3 60.3 + - - +
103B PHE* 4.2 5.8 + - + -
107B SER 3.1 14.1 - - - +
108B TYR* 4.2 2.5 - - + -
109B TYR* 4.2 9.7 + - - -
32G LEU* 3.9 17.9 - - + +
36G VAL* 3.4 29.2 - - + -
141G LEU* 3.4 24.9 - - - +
144G LEU 5.6 0.2 - - - +
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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