Contacts of the strand formed by residues 252 - 257 (chain I) in PDB entry 2QC8
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 CYS 252 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I MET* 3.6 35.9 - - - -
134I GLU 3.3 11.9 - - - -
135I GLN* 3.9 19.3 - - - +
218I LEU* 4.4 2.9 - - - -
251I GLY* 1.3 73.4 - - - +
253I HIS* 1.3 69.5 + - - +
254I THR* 3.1 12.0 + - - -
342I PRO* 2.9 19.6 + - - +
343I SER 3.1 23.1 - - - +
344I ALA* 4.0 4.0 - - - -
346I CYS* 4.1 8.5 - - - -
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Residues in contact with HIS 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I GLY 3.6 1.6 - - - +
133I MET* 3.2 4.2 - - - -
134I GLU* 2.9 49.9 + - + +
136I GLU* 4.5 3.9 + - - -
251I GLY* 4.7 1.6 - - - -
252I CYS* 1.3 79.1 - - - +
254I THR* 1.3 59.4 + - - +
255I ASN* 3.9 1.9 + - - -
338I GLU* 2.8 15.5 + - + +
339I ASP 3.3 7.0 - - - +
340I ARG* 3.3 41.9 + - - +
342I PRO* 4.8 0.4 - - - -
401I MN 4.3 2.7 - - - -
402I MN 2.3 25.6 + - - -
601I P3S 3.1 54.7 + - + -
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Residues in contact with THR 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I PHE* 4.1 10.8 - - + -
132I GLY 3.5 2.2 - - - -
133I MET* 3.5 28.8 - - + +
252I CYS 3.1 12.7 + - - -
253I HIS* 1.3 71.0 - - - +
255I ASN* 1.3 68.9 + - - +
256I PHE* 4.0 1.9 + - - +
337I PHE 3.7 0.9 - - - +
338I GLU* 4.4 0.2 - - - -
339I ASP* 2.7 40.2 + - - +
342I PRO* 3.7 5.3 - - - +
351I VAL* 3.5 19.6 - - + +
352I THR* 5.2 0.9 - - + -
355I LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I PHE* 3.3 8.5 - - - +
132I GLY 2.7 35.1 + - - +
134I GLU* 3.2 25.8 + - - +
253I HIS 4.0 4.0 + - - -
254I THR* 1.3 75.9 - - - +
256I PHE* 1.3 59.8 + - - +
326I PRO* 5.2 0.5 - - - +
336I TYR* 3.4 25.2 - - + -
337I PHE 3.2 4.9 - - - -
338I GLU* 3.3 24.8 - - - +
501I ADP 3.3 45.6 + - - +
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Residues in contact with PHE 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I PRO* 3.9 10.8 - - + -
130I TRP 3.4 7.0 - - - -
131I PHE* 3.4 30.5 - + + -
254I THR 4.8 1.1 - - - +
255I ASN* 1.3 76.2 - - - +
257I SER* 1.3 81.7 + - - +
258I THR* 4.0 18.2 - - + -
261I MET* 4.4 4.0 - - + +
336I TYR* 3.1 5.7 - - - +
337I PHE* 2.9 67.1 + + + +
355I LEU* 4.2 29.4 - - + -
356I ILE* 3.9 17.7 - - + -
359I CYS* 4.1 23.1 - - + -
360I LEU* 4.1 4.9 - - + -
501I ADP 3.9 1.9 - - - -
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Residues in contact with SER 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I PRO* 3.5 3.1 - - - +
130I TRP* 2.9 30.3 + - - +
256I PHE* 1.3 82.3 - - - +
258I THR* 1.3 64.6 + - - +
261I MET* 3.7 9.2 - - - -
262I ARG* 2.9 21.7 + - - +
335I GLY 3.3 25.8 - - - -
336I TYR* 3.6 0.4 - - - -
501I ADP 2.9 28.6 + - - -
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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