Contacts of the strand formed by residues 252 - 257 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D MET* 3.8 31.9 - - - -
134D GLU 3.2 17.9 - - - -
135D GLN* 4.0 19.3 - - - -
218D LEU* 4.2 5.2 - - - -
251D GLY* 1.3 73.7 - - - +
253D HIS* 1.3 66.7 + - - +
254D THR* 3.1 13.9 + - - -
342D PRO* 2.8 22.7 + - - +
343D SER 3.1 21.3 - - - +
344D ALA* 4.0 4.3 - - - +
346D CYS* 3.8 8.5 - - - -
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Residues in contact with HIS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLY 3.5 2.6 - - - +
133D MET* 3.4 3.5 - - - -
134D GLU* 3.0 50.3 + - + +
136D GLU* 4.5 2.9 + - - -
251D GLY* 4.7 1.8 - - - -
252D CYS* 1.3 77.2 - - - +
254D THR* 1.3 60.0 + - - +
255D ASN* 3.9 0.8 + - - -
299D ARG* 4.6 0.2 - - - -
338D GLU* 2.9 14.7 + - + +
339D ASP 3.4 7.2 - - - +
340D ARG* 3.3 41.4 + - + +
342D PRO* 4.8 0.2 - - - -
401D MN 4.3 2.7 - - - -
402D MN 2.4 24.7 + - - -
601D P3S 2.8 59.4 + - + +
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Residues in contact with THR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 4.1 11.9 - - + -
132D GLY 3.7 1.8 - - - -
133D MET* 3.3 25.2 - - + +
252D CYS 3.1 12.7 + - - -
253D HIS* 1.3 68.7 - - - +
255D ASN* 1.3 66.9 + - - +
256D PHE* 3.9 2.6 + - - +
337D PHE 3.9 1.0 - - - +
338D GLU* 3.6 0.3 - - - -
339D ASP* 2.7 44.2 + - - +
342D PRO* 3.8 5.6 - - - +
351D VAL* 3.6 23.9 - - + +
352D THR* 5.1 0.4 - - + -
355D LEU* 3.6 26.9 - - + -
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 3.2 7.8 - - - +
132D GLY 2.7 47.7 + - - +
134D GLU* 3.1 27.5 + - - +
253D HIS 4.0 2.0 + - - -
254D THR* 1.3 76.2 - - - +
256D PHE* 1.3 59.7 + - - +
326D PRO* 5.1 0.3 - - - +
336D TYR* 3.3 23.3 - - + -
337D PHE 3.2 3.8 - - - -
338D GLU* 3.2 25.5 - - - +
501D ADP 3.3 39.4 + - - +
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Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PRO* 3.8 15.5 - - + -
130D TRP 3.4 10.5 - - - -
131D PHE* 3.4 25.6 - + + -
254D THR 4.7 1.3 - - - +
255D ASN* 1.3 74.8 - - - +
257D SER* 1.3 79.5 + - - +
258D THR* 3.9 23.1 - - + -
261D MET* 4.6 5.2 - - + -
336D TYR* 3.3 5.0 - - - +
337D PHE* 2.9 70.1 + + + +
355D LEU* 4.3 27.1 - - + -
356D ILE* 4.3 12.8 - - + -
359D CYS* 4.1 23.6 - - + -
360D LEU* 4.6 4.7 - - + -
501D ADP 4.0 1.4 - - - -
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Residues in contact with SER 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PRO* 3.4 3.1 - - - +
130D TRP* 2.8 37.6 + - - +
256D PHE* 1.3 80.7 - - - +
258D THR* 1.3 63.3 + - - +
261D MET* 3.9 7.2 - - - -
262D ARG* 2.8 21.3 + - - +
335D GLY 3.3 24.7 - - - -
336D TYR* 3.6 1.1 - - - -
501D ADP 2.9 28.7 + - - -
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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