Contacts of the strand formed by residues 167 - 171 (chain A) in PDB entry 1A4I
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLY 3.8 1.2 + - - -
166A ARG* 1.3 69.5 - - - +
168A ALA* 1.3 75.2 + - - +
169A VAL* 3.9 6.5 - - + +
191A THR* 3.4 12.0 - - + +
193A THR* 2.7 30.3 + - - -
208A LYS* 3.6 41.2 - - + +
209A GLY 3.6 0.7 - - - -
210A ASP* 2.8 43.1 + - - +
211A ILE 3.3 4.4 + - - -
228A LYS* 6.0 0.4 - - - +
193B THR* 4.1 8.7 - - + -
205B GLU* 2.7 42.8 + - - +
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Residues in contact with ALA 168 (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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166A ARG 3.6 0.4 + - - -
167A HIS* 1.3 79.0 - - - +
169A VAL* 1.3 63.6 + - - +
170A VAL 4.2 0.4 - - - -
185A LEU* 3.9 28.9 - - + -
190A ALA* 4.0 16.6 - - + -
191A THR 2.8 10.2 + - - +
192A VAL* 3.3 6.3 - - + -
193A THR 2.8 25.1 + - - -
211A ILE* 3.2 19.3 - - + +
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Residues in contact with VAL 169 (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 HIS* 3.9 13.0 - - + +
168A ALA* 1.3 78.9 - - - +
170A VAL* 1.3 65.7 + - - +
171A VAL* 4.1 7.6 - - + -
185A LEU* 5.5 0.2 - - - +
193A THR* 3.3 9.9 - - - +
195A CYS* 4.0 27.1 - - - -
205A GLU 3.4 24.5 - - - +
206A VAL* 4.3 4.0 - - - +
208A LYS* 4.4 0.2 - - + -
209A GLY* 3.6 21.1 - - - +
211A ILE 2.9 7.8 + - - +
212A LEU* 3.3 22.8 - - + +
213A VAL* 2.9 25.8 + - - +
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Residues in contact with VAL 170 (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 VAL* 1.3 77.2 - - - +
171A VAL* 1.3 67.0 + - - +
172A GLY 3.6 17.7 + - - +
178A GLY* 3.7 22.2 - - - +
181A MET* 4.1 15.0 - - + -
182A HIS* 4.1 7.0 - - + -
185A LEU* 3.7 28.3 - - + -
192A VAL* 4.0 13.7 - - + -
193A THR 2.9 8.4 + - - +
194A THR* 3.4 9.0 - - - +
195A CYS* 2.9 27.4 + - - +
213A VAL* 3.3 10.8 - - + +
215A ALA* 6.0 1.1 - - + +
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Residues in contact with VAL 171 (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 VAL* 4.1 6.1 - - + -
170A VAL* 1.3 75.1 - - - +
172A GLY* 1.3 60.3 + - - +
195A CYS* 3.8 5.4 - - + -
202A LEU* 4.1 12.1 - - + -
206A VAL* 4.0 26.5 - - + -
212A LEU* 4.1 15.7 - - + -
213A VAL 2.8 12.3 + - - +
214A VAL* 4.3 10.3 - - + -
215A ALA* 2.8 34.5 + - - +
216A THR* 3.5 21.8 - - + -
221A MET* 3.8 11.0 - - + -
222A VAL* 4.8 1.8 - - + -
302A NDP 3.8 19.5 - - + -
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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