Contacts of the helix formed by residues 400 - 414 (chain A) in PDB entry 2O2C
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 ARG 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.6 12.3 - - + +
213A VAL* 3.8 24.8 - - + +
214A MET* 3.8 26.3 + - + +
217A GLU* 4.5 4.7 - - + -
397A TYR 4.7 1.0 + - - -
398A LEU* 3.2 1.2 - - - +
399A TRP* 1.3 132.1 + - + +
401A LEU* 1.3 62.0 + - - +
402A PRO* 3.5 2.2 - - - -
403A ALA* 3.6 33.3 + - + +
404A TYR* 3.3 20.8 + - - +
435A GLU* 5.5 4.9 + - - -
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Residues in contact with LEU 401 (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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214A MET* 3.9 17.3 - - + +
391A ILE* 4.5 2.2 - - + -
393A PRO* 4.4 5.6 - - + -
398A LEU* 3.0 46.5 + - + +
400A ARG* 1.3 75.7 - - - +
402A PRO* 1.4 68.7 - - + +
404A TYR* 3.1 4.0 + - + +
405A LEU* 2.9 42.3 + - + +
460A ILE* 3.8 28.5 - - + -
542A ILE* 4.5 9.6 - - + -
543A ILE* 3.5 31.6 - - + -
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Residues in contact with PRO 402 (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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391A ILE* 3.7 33.9 - - + +
393A PRO* 4.0 12.8 - - + -
398A LEU 3.7 4.9 - - - +
399A TRP* 3.6 16.2 - - - +
400A ARG 3.7 0.7 - - - -
401A LEU* 1.4 91.0 - - + +
403A ALA* 1.3 56.1 + - - +
405A LEU* 3.3 3.2 + - + +
406A GLN* 2.9 33.4 + - - +
432A ILE* 4.1 2.5 - - + +
433A PHE* 4.7 1.8 - - - -
434A GLY* 3.4 35.2 - - - +
435A GLU* 4.2 3.8 - - - +
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Residues in contact with ALA 403 (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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210A LEU* 3.7 22.6 - - + +
400A ARG* 3.6 44.7 + - - +
401A LEU 3.3 0.2 - - - -
402A PRO* 1.3 79.4 - - - +
404A TYR* 1.3 62.2 + - - +
406A GLN* 3.3 30.0 - - - +
407A GLN 3.5 4.0 + - - -
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Residues in contact with TYR 404 (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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210A LEU* 3.7 16.9 - - + +
211A GLY* 3.4 37.5 - - - -
214A MET* 4.0 21.3 - - + -
326A ARG* 3.6 25.3 + - - -
327A TYR* 4.8 0.3 - - - -
329A MET* 3.4 27.2 + - + +
400A ARG 3.3 11.8 + - - +
401A LEU* 3.1 8.4 + - + +
403A ALA* 1.3 79.4 - - - +
405A LEU* 1.3 70.2 - - + +
407A GLN* 3.2 9.1 + - + +
408A LEU* 3.1 35.1 + - + +
543A ILE* 3.6 30.5 - - + +
547A GLU* 4.4 3.6 + - - -
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Residues in contact with LEU 405 (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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391A ILE* 3.8 39.7 - - + -
401A LEU* 2.9 30.0 + - + +
402A PRO 3.9 3.8 - - - +
404A TYR* 1.3 85.3 - - + +
406A GLN* 1.3 58.6 + - - +
407A GLN 3.3 0.2 - - - -
408A LEU* 3.8 28.7 - - + -
409A ASP* 2.9 34.9 + - + +
432A ILE* 4.2 5.3 - - + +
543A ILE* 4.9 2.7 - - + -
546A TYR* 3.8 44.9 - - + -
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Residues in contact with GLN 406 (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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402A PRO* 2.9 23.2 + - - +
403A ALA* 3.3 20.9 - - - +
404A TYR 3.1 0.4 - - - -
405A LEU* 1.3 76.4 - - - +
407A GLN* 1.3 57.2 + - - +
410A MET* 2.9 46.5 + - - +
432A ILE* 2.9 41.3 + - + +
433A PHE* 4.3 7.8 - - - +
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Residues in contact with GLN 407 (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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206A GLY* 3.2 21.5 - - - +
207A GLY* 3.3 7.8 - - - +
210A LEU* 3.2 26.4 - - + +
326A ARG* 3.5 17.6 - - + +
403A ALA 3.5 1.6 + - - -
404A TYR* 3.2 11.5 + - + +
406A GLN* 1.3 77.3 - - - +
408A LEU* 1.3 65.9 + - - +
411A GLU* 3.0 42.4 + - + +
5001A G6Q 2.5 49.8 + - - -
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Residues in contact with LEU 408 (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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326A ARG* 3.8 21.5 - - - +
327A TYR* 3.4 38.4 - - + +
404A TYR* 3.1 28.0 + - + +
405A LEU* 3.8 27.8 - - + +
407A GLN* 1.3 77.3 - - - +
409A ASP* 1.3 57.8 + - + +
412A SER* 2.6 31.4 + - - -
543A ILE 4.5 0.9 - - - +
546A TYR* 4.0 5.8 - - + -
547A GLU* 3.9 33.9 - - + +
550A VAL* 4.0 9.6 - - + +
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Residues in contact with ASP 409 (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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405A LEU* 2.9 21.7 + - + +
408A LEU* 1.3 73.3 - - + +
410A MET* 1.3 59.7 + - - +
412A SER* 3.7 0.2 - - - -
413A ASN* 2.8 40.5 + - - +
429A GLY* 4.5 0.5 - - - -
430A PRO* 3.8 21.5 - - - +
432A ILE* 3.6 28.9 - - + +
546A TYR* 6.2 0.2 - - - -
549A LYS* 4.5 12.1 + - - +
550A VAL* 4.0 21.2 - - + +
553A GLN* 4.4 10.1 - - - +
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Residues in contact with MET 410 (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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406A GLN* 2.9 36.0 + - - +
409A ASP* 1.3 71.9 - - - +
411A GLU* 1.3 55.2 + - - +
414A GLY* 3.0 30.4 + - - +
429A GLY* 6.0 1.6 - - - -
430A PRO 3.5 18.8 - - - +
431A ILE* 4.0 27.6 - - + -
432A ILE* 3.4 34.5 - - + +
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Residues in contact with GLU 411 (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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326A ARG* 3.0 21.5 + - - +
406A GLN 3.9 0.2 + - - -
407A GLN* 3.0 33.8 + - + +
410A MET* 1.3 78.6 - - - +
412A SER* 1.3 60.1 + - - +
414A GLY 5.3 0.2 - - - +
415A LYS* 3.5 18.9 + - - -
563A ASP 3.8 1.0 - - - +
564A GLN* 4.2 11.3 - - + +
567A VAL* 4.1 19.0 - - + +
5001A G6Q 2.6 46.9 + - - +
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Residues in contact with SER 412 (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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326A ARG* 2.8 19.3 + - - +
327A TYR* 2.9 14.9 + - - -
408A LEU 2.6 24.9 + - - -
409A ASP 3.3 0.6 + - - -
410A MET 3.3 0.6 - - - -
411A GLU* 1.3 79.0 - - - +
413A ASN* 1.3 62.4 + - - +
415A LYS* 2.7 27.0 + - - +
550A VAL* 3.5 18.4 - - - -
561A SER* 3.3 25.1 + - - -
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Residues in contact with ASN 413 (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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409A ASP* 2.8 22.0 + - - +
412A SER* 1.3 74.7 - - - +
414A GLY* 1.3 55.5 + - - +
415A LYS 2.9 11.9 + - - -
428A THR* 3.3 5.7 + - - -
429A GLY* 2.9 26.0 + - - -
550A VAL* 3.1 37.2 + - - +
553A GLN* 3.9 13.1 + - - +
554A GLY* 3.8 7.3 - - - +
557A TRP* 3.9 15.9 - - + -
559A ILE* 3.6 15.6 - - + +
561A SER* 2.7 27.9 + - - -
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Residues in contact with GLY 414 (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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410A MET* 3.0 22.1 + - - +
411A GLU 4.6 0.4 - - - +
412A SER 3.6 2.0 - - - -
413A ASN* 1.3 72.4 - - - +
415A LYS* 1.3 67.9 + - - +
428A THR* 4.6 2.5 - - - -
429A GLY* 4.6 8.3 - - - -
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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