Contacts of the strand formed by residues 89 - 98 (chain B) in PDB entry 5SWW
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 ILE 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ARG* 4.1 2.1 - - - +
40B LEU* 3.1 55.1 + - + +
87B ALA 5.5 0.9 - - - +
88B GLN* 1.3 79.3 - - - +
90B TYR* 1.3 65.3 + - - +
119B HIS* 3.2 17.9 - - + +
121B ARG* 3.3 44.4 - - - +
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Residues in contact with TYR 90 (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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37B VAL* 4.0 19.3 - - + -
38B GLU 3.6 2.5 - - - +
39B ARG* 3.4 50.4 + - + -
40B LEU* 4.2 3.4 - - - -
50B GLN* 4.2 12.4 + - + -
51B HIS* 5.6 0.7 - + - -
83B GLN 4.6 2.1 + - - -
84B LEU* 3.8 32.6 - - + -
85B ASP* 3.1 54.9 + - + +
88B GLN* 3.9 13.8 + - + -
89B ILE* 1.3 76.4 - - - +
91B ARG* 1.3 60.5 + - - +
92B VAL* 4.0 0.8 + - + -
119B HIS* 3.0 13.3 + + - +
120B VAL* 3.4 15.0 - - + -
121B ARG* 2.9 27.9 + - - +
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Residues in contact with ARG 91 (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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36B GLU 3.6 1.6 - - - +
37B VAL* 3.5 2.5 - - - -
38B GLU* 2.3 73.7 + - + +
40B LEU* 4.0 20.6 - - + +
47B LYS* 3.5 19.6 - - - +
90B TYR* 1.3 72.3 - - - +
92B VAL* 1.3 64.3 + - - +
93B THR* 4.0 7.9 + - - +
121B ARG* 3.4 13.7 - - + +
123B ARG* 3.5 44.2 - - + +
203B GOL 4.8 1.8 + - - -
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Residues in contact with VAL 92 (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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35B TYR* 5.0 0.4 - - + -
36B GLU 3.3 8.5 - - - +
37B VAL* 3.8 22.4 - - + -
75B PHE* 3.6 32.8 - - + -
82B LEU* 5.7 0.7 - - + -
84B LEU* 5.4 5.4 - - + -
90B TYR* 5.1 1.8 - - + -
91B ARG* 1.3 76.9 - - - +
93B THR* 1.3 61.5 + - - +
94B TRP* 3.7 17.7 - - + +
113B PHE* 6.0 0.9 - - + -
120B VAL* 3.7 25.4 - - + -
121B ARG 2.9 8.9 + - - +
122B LEU* 3.3 13.1 - - + +
123B ARG* 2.9 27.5 + - - +
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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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34B CYS 3.5 1.7 - - - +
35B TYR* 3.2 6.8 - - - -
36B GLU* 2.9 46.2 + - - +
38B GLU* 4.7 2.9 + - - -
91B ARG* 4.3 7.4 + - - +
92B VAL* 1.3 73.1 - - - +
94B TRP* 1.3 63.5 + - - +
95B PHE* 3.6 29.1 - - + -
123B ARG* 2.6 45.8 + - + +
125B PHE* 3.8 15.9 - - + -
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Residues in contact with TRP 94 (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 LEU* 3.8 28.3 - - + -
34B CYS 3.7 2.5 - - - -
35B TYR* 4.2 2.7 - - + -
72B ALA* 3.8 34.3 - - + -
75B PHE* 3.4 50.0 - + + -
76B LEU* 4.8 4.3 - - + -
92B VAL* 3.7 8.9 - - + +
93B THR* 1.3 80.4 - - - +
95B PHE* 1.3 60.6 + - - +
96B ILE* 3.8 7.9 - - + +
100B PRO* 4.3 7.6 - - + -
110B VAL* 3.9 18.4 - - + -
122B LEU* 3.7 25.1 - - + -
123B ARG 2.9 11.0 + - - +
124B ILE* 3.6 42.2 - - + -
125B PHE* 2.9 34.0 + - - +
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Residues in contact with PHE 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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22B PHE* 3.3 14.7 - - + -
33B LEU* 3.5 1.5 - - - +
34B CYS* 2.9 54.4 + - + +
36B GLU* 3.2 30.3 - - + -
93B THR* 3.6 22.9 - - + -
94B TRP* 1.3 74.8 - - - +
96B ILE* 1.3 58.3 + - - +
125B PHE* 3.5 32.5 - + + -
153B MET* 4.0 14.1 - - + -
157B GLU* 3.8 17.5 - - + -
160B HIS* 3.8 17.5 - + - -
161B CYS* 3.4 31.2 - - - -
165B PHE* 4.2 2.5 - + - -
203B GOL 4.2 8.5 - - - -
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Residues in contact with ILE 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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22B PHE* 4.3 2.0 - - - -
31B THR* 3.9 13.9 - - + -
32B TYR 3.3 10.5 - - - +
33B LEU* 3.9 28.3 - - + +
71B ALA* 4.5 4.9 - - + -
72B ALA* 4.8 6.1 - - + +
94B TRP* 4.6 6.1 - - + -
95B PHE* 1.3 75.7 - - - +
97B SER* 1.3 62.7 + - - +
98B TRP 3.1 24.5 - - - +
100B PRO* 4.5 17.0 - - + -
124B ILE* 3.8 22.9 - - + -
125B PHE 2.9 15.0 + - - +
126B ALA* 3.9 6.5 - - + -
127B ALA* 3.0 25.8 + - - +
153B MET* 4.2 0.7 - - - +
0F C 4.6 5.8 - - - +
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Residues in contact with SER 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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21B ASN* 2.9 21.1 + - - +
22B PHE* 4.3 5.8 - - - -
30B LYS 4.2 1.4 + - - -
31B THR* 4.1 7.0 - - - -
32B TYR* 2.9 33.0 + - - -
95B PHE 4.2 0.2 + - - -
96B ILE* 1.3 72.3 - - - +
98B TRP* 1.3 59.6 + - - +
127B ALA* 3.6 9.3 - - - +
128B ARG* 2.6 63.6 + - - +
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Residues in contact with TRP 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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27B GLY* 3.4 17.3 - - - -
28B ARG 3.2 15.6 + - - -
30B LYS 3.4 8.5 + - - -
31B THR* 3.1 25.7 - - - +
96B ILE* 3.1 29.4 - - - +
97B SER* 1.3 77.8 - - - +
99B SER* 1.3 64.9 + - - +
126B ALA* 4.5 0.7 - - - -
128B ARG* 3.0 54.0 - - + +
129B ILE 3.4 14.8 - - - -
130B TYR* 3.5 31.6 - + + -
-1F T 3.4 49.1 - + - -
0F C 3.8 28.4 + + + +
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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