Contacts of the strand formed by residues 255 - 261 (chain A) in PDB entry 1A9Z
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 GLY 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLN* 3.5 17.9 - - - +
170A TRP 3.1 9.3 + - - +
171A SER* 3.6 1.0 - - - -
172A ILE 2.8 25.5 + - - +
254A PRO* 1.3 74.8 - - - +
256A VAL* 1.3 67.4 - - - +
257A HIS* 3.6 8.3 + - - -
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Residues in contact with VAL 256 (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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160A LEU 4.7 0.7 - - - +
161A THR* 4.0 28.0 - - + +
164A GLN* 3.5 36.3 + - + +
172A ILE* 3.1 12.3 - - + +
174A LEU* 3.6 35.4 - - + -
255A GLY* 1.3 72.5 - - - +
257A HIS* 1.3 63.1 + - - +
258A ILE* 3.8 14.9 + - + +
305A LYS* 5.8 0.2 + - - -
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Residues in contact with HIS 257 (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 SER* 3.5 15.1 + - - -
172A ILE 2.7 18.8 + - - +
173A ALA* 3.1 4.6 - - - +
174A LEU 2.8 24.0 + - - +
250A LEU* 3.7 40.6 - - + +
253A LYS* 2.6 35.7 + - + -
254A PRO 3.8 14.1 - - - -
255A GLY* 3.6 13.0 + - - -
256A VAL* 1.3 75.0 + - - +
258A ILE* 1.3 63.2 + - - +
259A TYR* 3.8 13.7 + - + +
305A LYS* 5.2 2.0 - - - +
410A PGE 4.3 16.5 - - - -
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Residues in contact with ILE 258 (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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138A GLU* 3.5 17.4 - - + +
161A THR* 5.8 0.7 - - - +
174A LEU* 3.4 28.5 - - + +
176A ARG* 3.5 45.8 - - - +
256A VAL* 3.8 21.2 + - + +
257A HIS* 1.3 77.5 - - - +
259A TYR* 1.3 62.9 + - - +
305A LYS* 2.7 43.1 + - - +
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Residues in contact with TYR 259 (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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138A GLU* 3.3 4.7 - - - -
174A LEU 3.0 7.0 + - - +
175A LEU* 3.5 21.9 - - + +
176A ARG* 2.9 24.0 + - - -
250A LEU* 3.9 13.2 - - + +
257A HIS* 3.8 28.8 - - + +
258A ILE* 1.3 78.9 - - - +
260A ASN* 1.3 69.0 + - - +
261A LEU* 3.6 8.1 + - + +
305A LYS* 3.3 36.1 - - + -
306A ALA* 3.7 23.1 - - + -
309A GLU* 2.4 33.1 + - + +
310A LEU* 3.9 22.2 - - + +
410A PGE 3.7 16.6 + - - -
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Residues in contact with ASN 260 (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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128A TYR* 2.6 35.4 + - - -
136A TYR 2.9 27.3 + - - -
138A GLU* 2.7 26.0 + - - +
176A ARG* 3.5 10.6 - - - +
178A PHE* 3.7 19.0 - - + -
259A TYR* 1.3 73.9 - - - +
261A LEU* 1.3 66.5 + - - +
262A GLY 3.9 1.7 + - - -
301A ALA* 4.1 5.2 - - + -
302A ASP 3.1 21.4 + - - +
303A ALA* 4.2 7.8 - - - +
306A ALA* 4.2 11.8 - - - +
312A TRP* 4.5 0.3 - - - -
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Residues in contact with LEU 261 (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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175A LEU* 4.1 23.6 - - + -
176A ARG 2.8 13.8 + - - +
177A TYR* 3.8 3.7 - - + -
178A PHE* 3.3 25.1 + - - -
234A ILE* 3.9 9.7 - - - +
239A LEU* 3.7 32.7 - - + +
242A GLY* 5.0 9.4 - - - -
243A HIS* 4.0 20.9 - - + +
259A TYR* 4.3 18.6 - - + +
260A ASN* 1.3 80.4 - - - +
262A GLY* 1.3 57.5 + - - +
306A ALA* 4.7 2.9 - - + -
310A LEU* 6.0 3.4 - - + -
312A TRP* 3.8 30.7 - - + -
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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