Contacts of the strand formed by residues 333 - 337 (chain B) in PDB entry 2QUH
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 ALA 333 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ARG 3.1 17.3 - - - +
142B ASP* 3.5 13.5 - - + +
143B MET 4.5 0.4 - - - +
146B VAL* 3.3 33.7 - - + -
304B GLN* 4.0 3.6 + - - +
305B CYS 2.8 11.8 + - - +
306B LEU* 3.8 5.8 - - + -
307B ILE* 2.7 30.3 + - - +
331B LYS 3.8 0.8 + - - -
332B PRO* 1.3 71.1 - - - +
334B LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B HIS* 3.0 9.9 - - - +
141B ARG* 2.8 46.5 + - + +
143B MET* 4.8 0.9 - - - +
306B LEU* 4.3 1.7 - - - +
307B ILE* 3.5 17.7 - - + +
309B CYS* 4.9 2.0 - - - -
314B ASP* 2.9 30.7 - - - +
317B PHE* 3.8 37.5 - - + -
321B ARG* 4.4 8.5 - - - -
332B PRO* 3.7 14.8 - - + +
333B ALA* 1.3 82.7 - - - +
335B LEU* 1.3 66.8 + - - +
336B HIS* 3.2 18.6 - - + -
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.0 15.3 - - + -
120B ILE* 5.6 2.0 - - + -
132B LEU* 5.4 4.0 - - + -
137B PHE* 3.0 24.1 - - + -
139B SER 3.5 2.0 - - - -
140B HIS* 3.9 15.0 - - + -
143B MET* 3.9 27.1 - - + -
179B PHE* 3.9 10.8 - - + -
183B LEU* 3.7 32.1 - - + -
306B LEU* 3.8 25.1 - - + -
307B ILE 3.1 6.6 + - - -
308B PRO* 4.1 7.2 - - + -
309B CYS 3.0 16.3 + - - -
334B LEU* 1.3 80.9 - - - +
336B HIS* 1.3 61.8 + - - +
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 5.5 0.4 - + - -
109B SER* 4.2 4.2 - - - -
137B PHE* 2.9 31.6 - - - -
138B PHE* 3.3 9.4 + - + -
139B SER* 2.8 50.5 + - - +
140B HIS* 4.0 2.0 - - - -
141B ARG* 3.8 15.4 + - - +
309B CYS* 3.3 14.3 + - - +
311B ILE* 4.0 25.7 - - + +
314B ASP* 2.8 43.0 + - + +
334B LEU* 3.2 23.6 - - + +
335B LEU* 1.3 70.8 - - - +
337B SER* 1.3 58.2 - - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.2 7.9 - - - -
137B PHE* 3.3 34.7 - - - -
138B PHE* 3.6 4.0 - - - -
175B ILE* 4.5 12.5 - - - +
176B PRO* 4.9 4.3 - - - +
309B CYS 3.0 6.2 + - - -
310B ALA* 3.2 19.9 + - - +
311B ILE* 2.9 27.4 + - - +
336B HIS* 1.3 73.9 - - - +
338B THR* 1.3 69.0 + - - +
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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