Contacts of the strand formed by residues 110 - 119 (chain B) in PDB entry 3GB9
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 THR 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLN 3.3 4.8 + - - -
27B VAL* 3.5 16.9 - - + -
28B ALA 2.9 25.3 + - - +
108B VAL* 3.0 7.9 - - - +
109B ASP* 1.3 94.8 + - - +
111B LEU* 1.3 68.4 + - - +
233B LEU* 4.7 1.1 - - - -
234B ARG* 3.2 33.6 + - + +
236B PHE* 4.0 28.7 - - + -
282B ILE* 3.8 12.2 - - + +
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Residues in contact with LEU 111 (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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28B ALA* 3.4 26.5 - - + +
30B ILE* 3.9 27.1 - - + -
100B VAL* 4.6 5.2 - - + -
103B PHE* 4.5 7.4 - - + -
110B THR* 1.3 75.1 - - - +
112B VAL* 1.3 64.5 + - - +
113B VAL* 3.5 24.5 - - + -
224B GLU* 4.1 17.0 - - + +
228B ALA* 3.7 24.9 - - + -
233B LEU* 4.2 15.4 - - + +
234B ARG 2.8 12.6 + - - +
235B VAL* 3.3 11.6 - - + +
236B PHE 3.1 24.4 + - - +
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Residues in contact with VAL 112 (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 VAL* 4.0 22.9 - - + -
28B ALA 2.8 11.0 + - - +
29B ILE* 4.0 19.7 - - + -
30B ILE 2.8 27.5 + - - +
110B THR* 4.4 0.2 - - + -
111B LEU* 1.3 75.3 - - - +
113B VAL* 1.3 69.5 + - - +
114B THR* 4.5 7.2 - - + -
236B PHE* 3.2 47.8 - - + +
237B GLY* 5.1 1.1 - - - -
238B PHE* 5.1 1.8 - - + -
275B VAL* 4.5 17.5 - - + -
279B MET* 4.4 6.1 - - + -
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Residues in contact with VAL 113 (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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30B ILE* 4.0 12.8 - - + -
84B ARG* 4.7 4.5 - - - +
111B LEU* 3.5 34.1 - - + -
112B VAL* 1.3 75.9 - - - +
114B THR* 1.3 64.3 + - - +
132B ILE* 4.6 6.1 - - + -
166B TYR* 4.9 2.7 - - + -
221B THR* 3.4 32.8 - - + -
224B GLU* 4.8 5.2 - - + -
225B VAL* 4.3 15.3 - - + -
235B VAL* 4.7 3.6 - - + -
236B PHE 3.0 12.2 + - - +
237B GLY* 2.9 37.6 - - - -
238B PHE 3.1 3.9 + - - -
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Residues in contact with THR 114 (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 ILE* 4.9 5.8 - - + -
30B ILE 2.9 13.1 + - - +
31B CYS* 3.4 3.7 - - - -
32B GLY 2.8 25.1 + - - -
35B LEU* 3.5 15.8 - - + +
38B LEU* 6.3 1.3 - - + -
84B ARG* 3.1 24.3 + - - -
112B VAL* 4.5 9.0 - - + -
113B VAL* 1.3 79.2 - - - +
115B ASN* 1.3 64.6 + - - +
238B PHE* 3.3 13.2 - - + +
271B LEU* 4.5 9.6 - - + -
275B VAL* 4.3 23.8 - - + -
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Residues in contact with ASN 115 (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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32B GLY* 4.1 2.4 - - - -
35B LEU* 4.4 6.6 - - - +
84B ARG* 4.0 0.2 - - - +
114B THR* 1.3 79.5 - - - +
116B ALA* 1.3 55.2 + - - +
117B ALA* 3.9 2.8 - - - +
132B ILE* 4.1 7.7 - - - +
192B TYR* 3.4 26.6 - - - +
220B SER* 3.8 1.1 - - - +
221B THR* 2.8 36.7 + - - +
238B PHE 3.1 4.3 + - - -
239B SER* 2.5 27.5 + - - -
240B LEU* 2.7 35.6 + - - +
271B LEU* 5.4 0.2 - - - +
290B SO4 3.2 20.4 - - - +
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Residues in contact with ALA 116 (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 SER* 4.2 22.6 - - - +
35B LEU* 6.0 0.2 - - + -
115B ASN* 1.3 74.0 - - - +
117B ALA* 1.3 59.4 + - - +
192B TYR* 5.4 0.2 + - - -
217B VAL 4.7 0.7 - - - +
218B GLY* 4.8 6.8 - - - -
240B LEU* 3.2 9.9 - - + -
242B THR* 3.7 26.7 - - + +
290B SO4 2.9 22.6 + - - +
300B A2F 5.3 3.0 + - - -
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Residues in contact with ALA 117 (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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115B ASN* 3.9 2.2 - - - +
116B ALA* 1.3 76.8 - - - +
118B GLY* 1.3 59.9 + - - +
192B TYR* 4.1 3.8 - - + -
216B ALA* 4.0 16.4 - - + -
217B VAL 3.4 16.4 - - - +
239B SER* 3.8 28.5 - - - +
240B LEU 2.7 7.6 + - - +
241B ILE* 3.4 6.2 - - + -
242B THR* 3.0 27.1 + - - -
300B A2F 3.9 6.1 - - - -
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Residues in contact with GLY 118 (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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117B ALA* 1.3 73.0 - - - +
119B GLY* 1.3 62.1 + - - -
120B LEU 3.6 0.2 + - - -
216B ALA* 3.2 8.2 - - - +
217B VAL* 2.9 35.3 + - - +
241B ILE* 4.6 0.7 - - - -
243B ASP* 3.4 10.3 - - - -
245B VAL* 3.8 13.2 - - - -
300B A2F 3.3 19.5 + - - -
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Residues in contact with GLY 119 (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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118B GLY* 1.3 70.9 - - - -
120B LEU* 1.3 60.3 + - - -
121B ASN 3.8 2.9 - - - -
124B PHE* 4.7 8.5 - - - -
215B ASP 3.9 4.7 - - - -
241B ILE* 3.9 19.5 - - - +
243B ASP 2.8 16.6 + - - -
244B LYS* 3.9 7.2 - - - +
245B VAL* 3.0 30.0 + - - +
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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