Contacts of the strand formed by residues 186 - 198 (chain B) in PDB entry 1F5J
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 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B GLN* 3.2 5.0 - - - +
38B TRP* 2.9 45.2 + - - +
71B ASN 3.6 6.5 - - - -
73B ASN* 3.4 16.3 - - - +
185B SER* 1.3 77.7 + - - +
187B SER* 1.3 61.8 + - - -
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Residues in contact with SER 187 (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 CYS 3.2 7.0 - - - -
37B GLN* 3.5 23.3 - - - -
38B TRP* 3.7 6.6 - - - -
70B TYR* 4.7 0.2 - - - -
71B ASN* 2.9 47.8 + - - +
72B PRO 4.1 0.2 - - - -
186B GLY* 1.3 76.3 - - - -
188B ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 188 (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 SER* 3.3 3.5 - - - -
36B CYS* 2.9 39.6 + - - +
68B ALA* 6.0 0.2 - - + -
69B THR 3.2 11.2 - - - +
70B TYR* 4.1 13.9 - - + -
71B ASN* 5.3 0.2 - - - -
179B VAL* 3.9 31.0 - - + -
187B SER* 1.3 77.9 - - - +
189B ASN* 1.3 60.7 - - - +
190B ILE* 4.1 4.9 - - + -
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Residues in contact with ASN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.4 7.1 - - - -
34B PHE 3.6 6.8 - - - +
35B SER* 3.3 23.6 - - - -
68B ALA* 3.2 2.8 - - - -
69B THR* 2.8 46.2 + - - +
188B ALA* 1.3 75.4 - - - +
190B ILE* 1.3 66.0 + - - +
191B THR* 3.4 26.6 + - - +
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Residues in contact with ILE 190 (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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29B TYR* 5.4 0.5 - - - -
32B GLY 4.1 18.2 - - - +
33B ARG* 3.4 6.8 - - - +
34B PHE* 2.7 61.1 + - + +
67B SER 3.6 4.0 - - - +
68B ALA* 3.8 15.0 - - + -
78B LEU* 4.7 3.1 - - + -
177B LEU* 3.5 33.7 - - + -
179B VAL* 3.7 30.5 - - + -
188B ALA* 4.3 2.9 - - + -
189B ASN* 1.3 80.9 - - - +
191B THR* 1.3 61.1 + - - +
192B GLN 3.7 14.1 - - - +
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Residues in contact with THR 191 (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 ARG* 3.2 26.5 + - - +
67B SER* 2.9 25.5 + - - -
68B ALA* 4.1 2.0 + - - -
69B THR* 5.1 5.6 - - - +
189B ASN* 3.4 33.6 + - - +
190B ILE* 1.3 73.2 - - - +
192B GLN* 1.3 61.2 - - - +
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Residues in contact with GLN 192 (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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31B GLN 5.2 0.2 - - - -
33B ARG* 3.9 5.7 - - - +
65B THR* 3.5 32.6 - - - +
66B TYR* 3.0 27.3 - - - +
67B SER* 2.8 41.7 + - - +
190B ILE* 3.5 6.4 - - - +
191B THR* 1.3 82.1 - - - +
193B ASN* 1.3 66.3 + - - +
194B THR* 3.9 15.2 + - - +
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Residues in contact with ASN 193 (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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13B TYR* 2.6 41.8 + - - -
31B GLN 4.1 7.1 + - - -
32B GLY 3.7 18.5 + - - +
48B THR* 3.0 40.4 + - - -
64B ILE* 3.5 14.4 - - - +
65B THR 3.6 3.1 - - - -
66B TYR* 4.5 0.2 - - - +
177B LEU* 3.5 22.8 - - + +
190B ILE* 4.3 0.9 - - + -
192B GLN* 1.3 75.6 - - - +
194B THR* 1.3 55.7 + - - +
195B PHE* 3.4 16.7 - - - -
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Residues in contact with THR 194 (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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13B TYR* 3.9 4.9 + - - +
63B ARG 3.6 1.0 - - - +
64B ILE* 3.2 5.9 - - - -
65B THR* 2.8 50.2 + - - -
192B GLN* 3.9 19.1 + - - +
193B ASN* 1.3 73.0 + - - +
195B PHE* 1.3 71.8 + - - +
196B SER* 5.5 2.6 - - - -
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Residues in contact with PHE 195 (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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13B TYR* 4.0 16.7 + + - +
49B GLY* 3.8 10.8 - - - -
50B LYS* 3.8 19.7 - - + -
52B TYR* 3.6 24.5 - - - -
62B ILE* 4.5 7.6 - - + -
63B ARG 3.5 3.4 - - - -
64B ILE* 3.5 31.0 - - + -
175B ILE* 3.4 30.7 - - + -
176B THR* 4.5 2.0 - - - -
193B ASN* 3.4 36.1 + - - -
194B THR* 1.3 88.6 - - - +
196B SER* 1.3 60.4 + - - +
197B GLN* 6.4 0.4 - - + -
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Residues in contact with SER 196 (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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61B THR 3.5 1.4 - - - +
62B ILE* 3.3 5.5 - - - +
63B ARG* 2.8 54.7 + - - +
65B THR* 6.1 0.9 - - - -
194B THR* 5.7 2.7 - - - -
195B PHE* 1.3 76.8 - - - +
197B GLN* 1.3 63.3 + - - +
198B SER* 5.6 1.6 + - - -
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Residues in contact with GLN 197 (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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114A ASP 4.2 13.7 - - - +
115A GLY* 4.4 0.9 - - - -
144A ARG* 4.2 13.7 + - - +
147A LYS 4.7 8.3 + - - -
148A ARG* 3.3 40.8 + - - +
149A THR 5.3 0.2 + - - -
150A SER 4.2 4.7 - - - +
52B TYR* 4.6 9.5 - - - -
59B LEU* 2.8 48.9 + - - +
61B THR 3.2 3.6 - - - -
62B ILE* 4.0 18.1 - - + +
195B PHE* 4.3 0.6 - - + -
196B SER* 1.3 77.5 + - - +
198B SER* 1.3 66.0 + - - +
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Residues in contact with SER 198 (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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115A GLY* 3.2 22.2 - - - -
144A ARG* 4.5 3.8 - - - +
59B LEU 4.8 0.2 - - - -
60B GLY* 3.5 1.8 - - - -
61B THR* 2.7 52.8 + - - +
63B ARG* 6.1 0.5 - - - -
196B SER* 5.6 2.0 + - - -
197B GLN* 1.3 79.0 - - - +
199B SER* 1.3 64.3 + - - +
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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