Contacts of the strand formed by residues 161 - 165 (chain B) in PDB entry 3GGE
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 HIS 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SO4 3.0 38.5 + - - -
138B TYR* 3.2 62.3 + + + +
139B ALA 3.5 5.4 - - - +
140B PHE* 3.8 25.9 - + + +
159B GLY 3.4 15.6 + - - -
160B ASP* 1.3 72.2 - - - +
162B ILE* 1.3 61.3 + - - +
163B GLU 3.6 0.4 + - - -
195B LEU* 3.2 7.2 - - - +
196B ILE* 2.9 43.3 + - + +
197B GLU 5.0 0.4 - - - -
198B PRO* 4.6 4.5 - - + +
136C VAL* 6.3 0.9 - - + -
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Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 5.4 1.3 - - + -
131B ILE* 4.3 26.9 - - + -
138B TYR* 4.8 7.5 - - - -
139B ALA* 3.1 22.0 + - + +
140B PHE* 4.8 1.1 - - - -
141B ILE* 4.3 22.2 - - + -
161B HIS* 1.3 71.3 - - - +
163B GLU* 1.3 64.3 + - - +
164B SER 3.7 14.6 - - - +
165B ILE* 4.1 1.1 - - + -
170B ILE* 3.4 36.4 - - + +
171B VAL* 4.4 3.3 + - - -
178B VAL* 4.3 7.9 - - + -
182B LEU* 5.2 0.2 - - + -
193B MET* 3.7 31.4 - - + -
194B LYS 4.0 5.4 - - - +
195B LEU* 3.7 16.4 - - + -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 2.9 25.3 - - - +
138B TYR* 5.2 2.2 - - + -
161B HIS 3.6 1.6 + - - -
162B ILE* 1.3 73.9 - - - +
164B SER* 1.3 68.2 + - - +
169B ASN* 3.7 9.0 + - - +
170B ILE* 3.0 21.6 + - - +
171B VAL* 3.7 17.8 + - + -
194B LYS* 3.0 22.9 + - + +
196B ILE* 3.2 28.0 - - + +
138C TYR* 3.8 14.0 + - - +
163C GLU* 5.4 1.9 - - - +
169C ASN* 2.8 26.8 + - - +
171C VAL* 4.3 4.7 - - + +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.5 3.3 - - - +
163B GLU* 1.3 85.3 - - - +
165B ILE* 1.3 67.5 + - - +
166B ASN 4.3 0.2 - - - -
167B GLY* 4.3 10.6 + - - -
168B GLU 3.3 25.1 - - - -
169B ASN* 4.2 2.7 - - - -
170B ILE* 4.3 3.6 - - - -
193B MET* 3.4 23.1 - - - +
194B LYS* 3.4 29.5 + - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 4.1 2.7 - - + -
164B SER* 1.3 79.1 - - - +
166B ASN* 1.3 75.7 + - + +
167B GLY 3.1 0.7 - - - -
168B GLU* 2.9 29.8 + - + +
170B ILE* 3.8 24.2 - - + +
178B VAL* 4.4 4.9 - - + +
181B LYS* 4.1 32.6 - - + -
182B LEU* 3.7 25.4 - - + -
185B LEU* 4.4 31.4 - - + -
191B PHE* 4.6 3.4 - - + -
192B THR 3.7 7.4 - - - +
193B MET* 4.1 17.3 - - + -
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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