Contacts of the strand formed by residues 257 - 264 (chain A) in PDB entry 2QQM
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A SER* 3.3 8.5 - - - -
163A PHE* 4.0 4.8 - - - -
167A TYR* 3.5 16.2 - - - -
192A PHE* 3.4 1.7 + - - -
193A ASP* 2.6 44.3 + - - +
194A LEU* 4.0 6.3 - - - -
255A LYS 3.3 0.8 - - - -
256A GLU* 1.3 78.8 - - - +
258A PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 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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158A ILE* 3.7 21.3 - - + -
159A LYS* 3.2 5.4 - - - +
160A SER* 3.0 60.7 + - - -
163A PHE* 3.6 8.8 - - - -
175A TYR* 3.8 25.1 - + - -
189A PHE* 3.6 19.5 - + + -
191A SER 3.2 12.3 - - - +
192A PHE* 3.7 16.8 - - + -
194A LEU* 4.5 10.8 - - + -
211A LEU* 3.9 17.5 - - + -
245A MET* 4.2 15.3 - - + -
247A PHE* 3.9 21.8 - + - -
257A GLY* 1.3 76.6 - - - +
259A SER* 1.3 64.0 + - - +
260A ALA* 5.6 0.2 - - + -
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Residues in contact with SER 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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157A VAL* 3.9 15.8 - - - +
158A ILE 3.5 5.2 - - - -
159A LYS* 4.0 6.8 - - - +
163A PHE* 3.6 26.5 - - - -
189A PHE* 3.6 2.0 - - - -
190A GLU* 2.8 47.9 + - - -
191A SER* 2.9 17.5 + - - +
258A PHE* 1.3 76.7 - - - +
260A ALA* 1.3 56.4 + - - +
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Residues in contact with ALA 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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157A VAL* 3.3 5.5 - - - +
158A ILE* 2.7 43.2 + - + +
187A LEU* 3.7 19.4 - - + +
188A GLU 3.1 16.8 - - - +
189A PHE* 3.7 28.0 - - + -
190A GLU* 4.2 2.5 - - - +
245A MET* 6.0 0.2 - - + -
258A PHE* 5.1 0.2 - - + -
259A SER* 1.3 76.2 + - - +
261A ASN* 1.3 59.2 + - - +
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Residues in contact with ASN 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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156A GLY 3.2 11.2 - - - +
157A VAL* 4.0 14.6 - - + -
187A LEU* 3.9 2.2 - - - -
188A GLU* 3.0 33.1 + - - +
190A GLU* 3.7 20.8 - - - +
260A ALA* 1.3 75.2 - - - +
262A TYR* 1.3 61.7 + - - +
1B NAG 1.5 70.8 + - + +
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Residues in contact with TYR 262 (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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151A TYR* 3.2 36.8 - + + +
153A THR* 2.8 40.9 + - - -
154A PRO 3.8 2.5 - - - -
155A SER* 3.2 40.5 + - - -
156A GLY* 2.8 38.7 + - - +
158A ILE* 4.2 17.5 - - + -
177A VAL* 3.7 25.1 - - + -
185A ILE* 4.0 13.9 - - + -
186A ILE 3.0 13.9 - - - +
187A LEU* 3.7 11.7 - - + -
261A ASN* 1.3 74.2 - - - +
263A SER* 1.3 68.7 + - - +
264A VAL* 4.5 3.8 - - + -
1B NAG 3.3 9.2 - - - +
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Residues in contact with SER 263 (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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154A PRO 3.4 8.7 - - - -
155A SER* 4.1 7.6 - - - -
184A GLU 4.1 0.2 - - - +
185A ILE* 3.7 2.9 - - - +
186A ILE* 2.9 36.1 + - - +
262A TYR* 1.3 73.1 + - - +
264A VAL* 1.3 67.0 + - - +
265A LEU* 5.9 2.9 - - - -
1B NAG 2.6 30.5 - - - +
2B FUC 4.0 9.7 + - - -
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Residues in contact with VAL 264 (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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154A PRO* 3.0 28.2 + - + +
177A VAL* 5.3 0.2 - - + -
179A ALA* 4.0 14.4 - - + -
180A PRO* 3.9 35.7 - - + +
183A SER* 3.7 13.7 - - - -
184A GLU 3.3 13.0 - - - +
185A ILE* 4.2 8.1 - - + -
262A TYR* 4.5 8.5 - - + -
263A SER* 1.3 78.8 - - - +
265A LEU* 1.3 77.8 + - - +
266A GLN* 3.8 11.9 + - + +
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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