Contacts of the helix formed by residues 425 - 435 (chain B) in PDB entry 2G4C
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 LEU 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389B ARG* 4.9 16.2 - - - +
423B SER 3.6 1.4 + - - -
424B SER* 1.3 81.0 + - - +
426B GLU* 1.3 72.6 + - + +
427B GLN 3.2 0.7 - - - -
428B LEU* 3.5 15.9 - - + -
429B TYR* 2.8 66.9 + - + +
442B LEU* 4.0 26.2 - - + -
463B LYS* 5.4 8.1 - - + +
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Residues in contact with GLU 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B SER* 2.8 16.8 + - - +
425B LEU* 1.3 87.8 + - + +
427B GLN* 1.3 58.5 + - + +
428B LEU 3.0 5.2 - - - -
429B TYR* 4.3 5.4 - - - +
430B SER* 3.0 34.1 + - - -
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Residues in contact with GLN 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B MET* 5.7 3.0 - - - -
423B SER* 3.1 27.0 + - - +
424B SER* 3.3 19.7 + - - +
425B LEU 3.2 0.2 - - - -
426B GLU* 1.3 80.3 - - + +
428B LEU* 1.3 56.1 + - - +
430B SER* 5.3 1.6 - - - -
431B LYS* 2.8 32.4 + - - +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ASP* 3.2 28.0 - - + +
422B GLN 3.9 8.7 - - - +
423B SER* 3.7 25.6 - - - +
425B LEU* 3.4 25.0 + - + +
426B GLU 3.0 0.6 - - - -
427B GLN* 1.3 81.0 - - - +
429B TYR* 1.3 67.5 + - + +
431B LYS* 4.2 10.1 - - + +
432B TYR* 3.1 61.8 + - + +
442B LEU* 6.0 2.7 - - + -
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Residues in contact with TYR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 2.8 52.0 + - + +
426B GLU* 4.3 4.5 - - - +
428B LEU* 1.3 88.7 - - + +
430B SER* 1.3 66.2 + - - +
431B LYS 3.1 1.7 + - - -
432B TYR* 3.3 5.1 + - - +
433B ASP* 2.9 25.5 + - - +
440B THR* 3.6 40.2 + - + -
442B LEU* 4.2 14.3 - - + +
454B HIS* 5.1 7.3 + - - -
456B ARG* 3.2 50.3 + - + +
463B LYS* 4.4 19.4 - - + +
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Residues in contact with SER 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ARG* 5.2 4.9 - - - +
370B LYS* 4.4 22.5 + - - +
426B GLU 3.0 17.8 + - - -
427B GLN* 5.3 1.1 - - - -
429B TYR* 1.3 77.4 - - - +
431B LYS* 1.3 59.5 + - - +
433B ASP* 2.9 30.7 - - - +
434B GLU* 3.2 10.5 + - - +
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Residues in contact with LYS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.8 37.6 - - - +
423B SER* 6.1 2.2 - - - -
427B GLN* 2.8 35.2 + - - +
428B LEU* 4.1 10.6 - - + +
429B TYR 4.1 0.6 - - - +
430B SER* 1.3 74.4 - - - +
432B TYR* 1.3 78.1 + - + +
433B ASP 2.9 4.0 - - - -
434B GLU* 2.7 40.7 + - - +
435B MET* 3.1 12.8 + - + +
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Residues in contact with TYR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ALA* 3.2 27.1 - - + +
386B ASP* 3.1 19.2 + - - -
414B TRP* 3.7 24.0 + + - -
416B GLY* 4.3 0.9 - - - -
428B LEU* 3.1 42.3 + - + +
429B TYR* 3.3 8.3 + + - +
431B LYS* 1.3 96.0 - - + +
433B ASP* 1.3 59.0 + - - +
434B GLU 3.1 0.2 - - - -
435B MET* 3.3 13.9 + - - -
436B SER 3.0 3.8 + - - -
437B ILE* 3.0 48.5 + - + +
440B THR* 3.5 36.3 - - + +
456B ARG* 6.1 0.4 - - - +
458B ARG* 5.4 0.2 - - - -
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ARG* 2.9 32.6 + - + +
370B LYS 5.9 0.4 - - - +
371B VAL* 2.9 34.2 - - + +
372B LEU 2.7 28.1 + - - +
429B TYR 2.9 19.7 + - - +
430B SER* 2.9 20.7 + - - +
431B LYS 2.9 0.6 - - - -
432B TYR* 1.3 76.6 - - - +
434B GLU* 1.3 55.3 + - - +
436B SER* 3.2 8.1 + - - -
456B ARG* 3.3 18.1 + - - -
458B ARG* 3.5 15.4 - - - +
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 3.5 29.0 - - + +
75B ARG* 5.3 5.2 - - - +
76B ARG* 2.8 39.0 + - + +
78B PHE* 3.6 3.6 - - - -
370B LYS* 3.3 45.0 - - + +
371B VAL* 4.5 0.4 - - - +
372B LEU* 2.9 32.1 - - - +
430B SER* 3.8 7.2 - - - +
431B LYS* 2.7 14.5 + - - +
433B ASP* 1.3 74.7 - - - +
435B MET* 1.3 52.1 + - - +
436B SER 2.6 15.8 + - - -
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Residues in contact with MET 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.9 31.4 - - + +
78B PHE* 3.8 11.4 - - - -
102B LEU* 4.4 12.2 - - + +
380B PRO* 3.7 17.7 - - - +
381B ILE* 4.1 17.6 - - + +
414B TRP* 3.6 40.2 - - + -
431B LYS* 3.1 13.6 + - + +
432B TYR* 3.3 32.1 + - - +
434B GLU* 1.3 76.9 - - - +
436B SER* 1.3 68.3 + - - +
437B ILE* 3.2 13.0 + - + +
199D LEU* 4.8 9.9 - - + -
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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