Contacts of the strand formed by residues 159 - 167 (chain A) in PDB entry 6QPA
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 THR 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 5.7 1.1 - - - +
158A ARG* 1.3 78.6 + - - +
160A VAL* 1.3 71.3 + - - +
161A VAL* 4.1 17.3 - - + -
257A ILE 3.9 0.2 - - - +
258A GLU* 3.3 4.9 - - - +
259A TRP* 2.9 34.4 + - + +
260A GLU 4.3 0.2 + - - -
261A SER* 3.1 12.7 - - - -
262A PRO* 3.0 37.9 - - + +
265A ALA* 4.1 12.3 - - + -
298A PHE* 4.3 9.9 - - + -
299A PHE 3.7 10.2 + - - +
300A SER* 5.3 0.2 - - - +
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Residues in contact with VAL 160 (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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46A GLU* 5.9 0.9 - - - +
48A LEU* 4.1 35.7 - - + -
158A ARG* 4.2 5.4 + - - +
159A THR* 1.3 78.7 - - - +
161A VAL* 1.3 69.1 + - - +
162A ILE* 4.4 3.4 - - + -
256A HIS* 3.4 32.5 - - + +
257A ILE 3.6 2.9 - - - +
258A GLU* 4.0 22.9 - - + +
298A PHE* 3.6 0.9 - - - -
299A PHE* 2.7 45.8 + - + +
301A PRO* 4.3 14.6 - - + -
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Residues in contact with VAL 161 (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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159A THR* 4.1 2.9 - - + -
160A VAL* 1.3 76.5 - - - +
162A ILE* 1.3 62.8 + - - +
255A VAL 3.4 0.7 - - - +
256A HIS* 3.5 2.6 - - - -
257A ILE* 2.8 42.5 + - + +
259A TRP* 4.2 6.5 - - + +
265A ALA* 3.9 20.2 - - + -
269A LEU* 3.7 13.2 - - + -
296A TYR* 3.2 37.0 - - + -
297A MET 3.3 5.4 - - - +
298A PHE* 3.5 37.2 - - + -
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Residues in contact with ILE 162 (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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48A LEU* 4.0 9.4 - - + -
77A PHE* 3.6 25.8 - - + -
79A TYR* 3.3 26.0 - - + +
160A VAL* 4.4 5.8 - - + -
161A VAL* 1.3 78.3 - - - +
163A GLY* 1.3 61.6 + - - +
164A ASP* 3.8 0.9 + - + +
199A MET* 5.2 0.7 - - + -
254A LEU* 3.8 41.3 - - + -
255A VAL 3.4 5.4 - - - +
256A HIS* 4.8 2.5 - - - +
295A TYR 3.3 3.8 - - - +
296A TYR* 3.3 2.6 - - - -
297A MET* 3.0 33.7 + - + +
299A PHE* 3.6 29.6 - - + -
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Residues in contact with GLY 163 (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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162A ILE* 1.3 73.4 - - - +
164A ASP* 1.3 59.9 + - - -
165A HIS* 2.9 15.7 + - - -
253A TYR 3.4 2.8 - - - +
254A LEU* 3.4 1.0 - - - -
255A VAL 2.8 38.2 + - - -
295A TYR 3.2 7.4 - - - -
296A TYR* 3.3 28.2 - - - -
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Residues in contact with ASP 164 (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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162A ILE* 3.8 2.5 + - + +
163A GLY* 1.3 70.3 - - - -
165A HIS* 1.3 62.9 + - - +
166A TRP* 3.5 20.1 + - - -
252A GLN* 3.1 32.8 + - - +
253A TYR 3.9 2.2 - - - -
254A LEU* 3.9 9.1 - - + +
292A LYS* 4.1 0.7 - - - +
293A GLY* 3.8 5.4 - - - -
294A PRO* 3.5 6.9 - - - +
295A TYR* 2.7 44.6 + - + +
297A MET* 6.3 2.7 - - - -
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Residues in contact with HIS 165 (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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163A GLY* 2.9 35.6 + - - -
164A ASP* 1.3 73.4 + - - +
166A TRP* 1.3 62.7 + - - +
167A VAL* 4.0 0.7 - - + -
175A PHE* 3.8 24.9 - + + -
251A THR 3.7 0.5 - - - +
252A GLN* 3.3 5.0 - - - +
253A TYR* 2.8 41.3 + - + +
255A VAL* 3.5 24.3 - - + +
282A HIS* 5.0 1.4 + - - -
286A VAL* 3.9 11.1 - - + +
290A LEU* 3.8 28.9 - - + -
292A LYS 3.6 3.8 - - - -
294A PRO* 3.3 26.5 - - + +
296A TYR* 3.8 16.7 + - - -
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Residues in contact with TRP 166 (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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164A ASP* 3.5 22.1 + - - -
165A HIS* 1.3 80.9 - - - +
167A VAL* 1.3 55.6 + - - +
248A GLN* 3.4 35.1 - - - +
249A THR 5.5 0.2 - - - -
250A PRO* 4.0 29.6 - - + -
251A THR 3.4 4.0 - - - -
252A GLN* 4.1 12.7 - - + +
290A LEU* 3.3 5.4 - - - -
291A ASP* 2.7 33.0 + - + -
292A LYS* 3.0 66.1 + - + +
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Residues in contact with VAL 167 (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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165A HIS* 4.7 2.0 - - + -
166A TRP* 1.3 75.2 - - - +
168A MET* 1.3 78.2 + - - +
169A ASP* 3.5 0.9 + - - -
171A HIS 3.6 26.0 - - - +
172A GLU* 3.8 9.6 - - + +
175A PHE* 3.5 30.1 - - + -
250A PRO* 3.3 18.0 - - - +
251A THR* 2.9 20.0 + - - +
253A TYR* 3.5 29.6 - - + -
289A HIS 3.4 10.1 - - - +
290A LEU* 4.0 5.8 - - + -
291A ASP* 4.2 2.2 - - - -
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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