Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 3GA5
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 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B ILE* 3.9 25.8 - - + -
127B TRP* 3.7 37.7 - - + -
140B LYS* 1.3 71.2 - - - +
142B GLN* 1.3 62.7 + - - +
143B TYR* 3.7 15.9 + - + -
166B LEU* 4.3 13.5 - - + -
171B ILE* 3.7 22.4 - - + -
172B GLN 3.0 9.0 + - - +
173B THR* 3.5 7.3 - - + -
174B GLU 2.8 27.9 + - - +
205B GLU* 3.7 3.1 - - - -
206B VAL* 3.6 31.9 - - + -
208B ILE* 5.8 0.9 - - + -
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Residues in contact with GLN 142 (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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136B ASN* 3.3 10.8 - - - +
138B ASP* 3.0 21.9 + - - -
140B LYS* 3.4 6.1 - - - +
141B ILE* 1.3 71.3 - - - +
143B TYR* 1.3 57.2 + - - +
174B GLU* 2.4 50.2 + - - +
176B LEU* 4.0 16.4 - - + -
203B LYS* 3.6 21.8 - - + +
205B GLU* 2.9 45.7 + - - +
206B VAL 3.4 1.7 + - - -
501B CA 2.4 29.8 - - - -
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Residues in contact with TYR 143 (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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141B ILE* 3.7 22.2 - - + -
142B GLN* 1.3 74.2 - - - +
144B VAL* 1.3 72.6 + - - +
145B LEU* 4.0 25.5 - - + +
163B VAL* 3.4 24.7 - - + +
166B LEU* 6.1 0.4 - - + -
173B THR* 3.8 21.7 + - + -
174B GLU 3.0 39.8 + - - -
175B GLN* 3.3 35.2 + - + +
176B LEU* 2.9 29.3 + - - +
177B ALA 3.8 0.9 + - - -
204B ILE* 5.1 0.2 - - - -
205B GLU 5.0 0.4 - - - +
206B VAL 3.2 13.9 - - - +
208B ILE* 3.8 25.6 - - + -
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Residues in contact with VAL 144 (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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143B TYR* 1.3 80.9 - - - +
145B LEU* 1.3 59.0 + - - +
176B LEU* 4.2 6.5 - - + -
177B ALA* 3.3 22.2 - - + +
192B MET* 4.1 2.7 - - + -
195B TRP* 3.7 35.2 - - + -
204B ILE* 4.0 33.0 - - + +
206B VAL 3.1 2.9 + - - +
207B VAL* 3.7 30.5 - - + +
208B ILE* 3.0 27.7 + - - +
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Residues in contact with LEU 145 (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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143B TYR* 4.0 23.5 - - + -
144B VAL* 1.3 74.9 - - - +
146B LEU* 1.3 66.6 + - - +
147B LYS* 3.7 22.0 - - + +
159B THR* 3.6 37.2 - - + +
162B VAL* 4.3 13.2 - - + -
163B VAL* 5.2 1.6 - - + -
177B ALA 3.0 8.2 + - - +
178B LEU* 3.3 21.6 - - + -
179B ASP 3.2 25.5 + - - +
195B TRP* 3.6 3.7 - - - -
208B ILE* 3.2 29.2 - - + +
210B ASN* 3.9 3.8 - - - +
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Residues in contact with LEU 146 (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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145B LEU* 1.3 71.8 - - - +
147B LYS* 1.3 61.4 + - - +
179B ASP 3.5 3.6 - - - +
181B ALA* 4.2 7.2 - - + -
188B ALA* 4.1 18.8 - - + +
191B LYS* 3.7 24.0 - - + -
192B MET* 4.7 2.2 - - - -
195B TRP* 3.7 29.8 - - + -
207B VAL* 4.2 14.4 - - + -
208B ILE 2.8 11.2 + - - +
209B ALA* 4.2 8.1 - - + -
210B ASN* 2.9 30.1 + - - +
214B MET* 3.2 26.4 - - + +
218B ALA* 3.9 28.0 - - + -
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Residues in contact with LYS 147 (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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145B LEU* 3.7 10.0 - - + +
146B LEU* 1.3 71.9 - - - +
148B GLY* 1.3 74.3 + - - +
150B PRO* 4.8 9.6 - - + +
155B ALA* 4.1 8.5 - - + -
156B GLU* 3.1 41.9 + - - -
159B THR* 3.6 23.0 - - + +
178B LEU* 4.3 18.7 - - + +
179B ASP 2.9 17.4 + - - +
180B THR* 3.1 8.1 + - - -
181B ALA 3.0 23.0 + - - -
210B ASN* 3.3 14.1 - - - +
214B MET* 3.4 8.0 - - - +
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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