Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 3PE7
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 SER 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.6 28.3 + - - -
171A MET* 3.6 22.3 - - - +
172A ARG 3.3 7.2 - - - -
173A VAL* 4.3 4.0 - - - -
178A GLY 3.7 1.0 + - - -
179A GLU* 1.3 76.5 - - - +
181A THR* 1.3 64.5 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A MET* 3.6 6.8 - - - -
172A ARG* 2.8 78.1 + - - +
179A GLU* 5.4 1.4 - - - +
180A SER* 1.3 77.7 + - - +
182A VAL* 1.3 74.2 + - - +
183A ILE 3.5 0.5 + - - -
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ARG* 4.1 28.7 - - + +
170A LEU 3.8 3.4 - - - -
171A MET* 3.6 21.3 - - + -
181A THR* 1.3 82.6 - - - +
183A ILE* 1.3 64.3 + - - +
184A LEU* 3.5 28.0 - - - +
185A GLN* 4.1 11.2 - - + +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.1 8.1 - - + -
170A LEU* 2.8 35.5 + - + +
172A ARG* 3.7 41.1 - - + +
181A THR 4.2 0.2 - - - +
182A VAL* 1.3 75.3 - - - +
184A LEU* 1.3 61.4 + - + +
203A VAL* 4.5 6.1 - - + -
221A ILE* 4.1 17.7 - - + +
222A ASN 3.8 14.8 - - - +
223A GLU* 3.6 34.3 - - + +
224A ASP 5.4 1.1 - - - -
225A GLY* 3.4 23.8 - - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A CYS 4.0 0.2 - - - +
169A ARG* 3.1 5.2 - - - +
170A LEU* 2.8 41.8 + - + -
182A VAL* 3.5 4.7 - - - +
183A ILE* 1.3 82.2 - - - +
185A GLN* 1.3 66.0 + - - +
186A GLU* 3.8 29.4 - - + +
190A LEU* 3.9 16.3 - - + +
205A PHE* 3.6 38.1 - - + -
221A ILE* 4.2 16.2 - - + -
225A GLY 5.8 0.4 - - - +
228A MET* 3.9 16.4 - - + -
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Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.8 6.3 - - - -
145A ARG* 3.7 13.5 - - - +
167A CYS* 3.6 28.1 - - - -
168A CYS 3.3 12.1 - - - +
169A ARG* 3.5 27.0 + - + +
182A VAL* 4.1 12.1 - - + +
184A LEU* 1.3 78.9 - - - +
186A GLU* 1.3 70.5 + - - +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A CYS* 3.5 1.0 - - - -
168A CYS 2.9 31.5 + - - +
184A LEU* 3.8 23.0 - - + +
185A GLN* 1.3 81.0 - - - +
187A ASN* 1.3 63.3 + - - +
188A GLN* 2.9 42.5 + - + +
190A LEU* 3.8 19.0 - - + +
207A HIS* 4.2 3.5 + - - -
228A MET* 3.5 27.4 - - - +
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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