Contacts of the strand formed by residues 252 - 257 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G MET* 3.4 34.5 - - - -
134G GLU 3.2 12.6 - - - +
135G GLN* 3.8 22.7 - - - +
218G LEU* 4.1 5.6 - - - -
251G GLY* 1.3 72.6 - - - +
253G HIS* 1.3 68.7 + - - +
254G THR* 3.2 10.4 + - - -
342G PRO* 2.7 19.6 + - - +
343G SER 3.3 20.2 - - - +
344G ALA* 3.8 5.6 - - - +
346G CYS* 4.0 7.9 - - - -
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Residues in contact with HIS 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G GLY 3.6 2.3 - - - +
133G MET* 3.4 3.3 - - - -
134G GLU* 2.9 49.5 + - + +
136G GLU* 4.5 2.0 - - - -
251G GLY* 4.6 2.7 - - - -
252G CYS* 1.3 80.0 - - - +
254G THR* 1.3 60.0 + - - +
255G ASN* 4.0 0.4 + - - -
338G GLU* 2.9 12.9 + - + +
339G ASP 3.5 10.3 - - - +
340G ARG* 3.5 38.2 + - - +
342G PRO* 4.7 1.1 - - - -
401G MN 4.1 2.9 - - - -
402G MN 2.5 19.8 + - - -
601G P3S 2.8 59.9 + - + -
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Residues in contact with THR 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G PHE* 4.0 9.0 - - + -
132G GLY 3.7 2.2 - - - -
133G MET* 3.5 24.8 - - + +
252G CYS 3.2 11.9 + - - -
253G HIS* 1.3 70.6 - - - +
255G ASN* 1.3 69.1 - - - +
256G PHE* 4.2 1.6 + - - +
337G PHE 3.9 0.3 - - - +
338G GLU* 4.6 0.2 - - - -
339G ASP* 2.6 47.6 + - - +
342G PRO* 3.9 5.2 - - - +
351G VAL* 3.4 23.7 - - + +
352G THR* 5.1 0.2 - - + -
355G LEU* 3.7 28.0 - - + -
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Residues in contact with ASN 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G PHE* 3.2 7.6 - - - -
132G GLY 2.7 48.6 + - - +
134G GLU* 3.2 24.8 + - - +
253G HIS 4.0 3.2 + - - -
254G THR* 1.3 77.5 - - - +
256G PHE* 1.3 61.8 + - - +
326G PRO* 5.2 0.2 - - - +
336G TYR* 3.3 23.3 - - + -
337G PHE 3.3 5.2 - - - +
338G GLU* 3.5 20.7 - - - +
501G ADP 3.4 40.4 + - - +
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Residues in contact with PHE 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G PRO* 3.9 15.9 - - + -
130G TRP 3.3 6.5 - - - -
131G PHE* 3.2 39.0 - + + -
254G THR 5.0 1.8 - - - +
255G ASN* 1.3 75.2 - - - +
257G SER* 1.3 73.1 + - - +
258G THR* 4.1 16.4 - - + -
261G MET* 4.3 11.8 - - + +
336G TYR* 3.3 5.1 - - - +
337G PHE* 2.9 67.2 + + + +
355G LEU* 4.5 20.4 - - + -
356G ILE* 4.1 14.8 - - + -
359G CYS* 4.2 24.0 - - + -
360G LEU* 4.3 5.4 - - + -
501G ADP 4.2 1.4 - - - -
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Residues in contact with SER 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G PRO* 3.5 2.4 - - - +
130G TRP* 2.8 35.5 + - - +
256G PHE* 1.3 78.5 - - - +
258G THR* 1.3 61.8 + - - +
261G MET* 3.7 8.1 - - - -
262G ARG* 3.0 21.4 + - - -
335G GLY 3.2 26.9 - - - -
336G TYR* 3.6 0.7 - - - -
501G ADP 2.6 32.1 + - - -
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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