Contacts of the helix formed by residues 434 - 442 (chain G) in PDB entry 3SRF
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 GLY 434 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431G THR* 2.7 22.7 + - - -
432G GLU 3.7 0.4 - - - -
433G SER* 1.3 73.7 + - - +
435G ARG* 1.3 64.4 + - - +
436G SER 3.2 2.9 - - - -
437G ALA* 3.0 16.4 + - - +
438G HIS* 3.0 33.2 + - - -
458G THR* 3.8 11.9 - - - +
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Residues in contact with ARG 435 (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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408G MET* 4.7 3.1 - - + +
433G SER* 2.7 40.4 + - - -
434G GLY* 1.3 74.6 - - - +
436G SER* 1.3 61.6 + - - +
438G HIS* 3.8 11.3 + - - +
439G GLN* 3.2 30.7 + - - +
519G GLY 3.9 14.1 + - - -
520G PHE* 5.9 1.0 - - - +
531G PO4 2.9 22.7 + - - +
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Residues in contact with SER 436 (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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408G MET* 3.4 20.9 - - - +
429G VAL* 3.8 9.7 - - - +
431G THR* 4.3 0.2 - - - -
435G ARG* 1.3 72.7 - - - +
437G ALA* 1.3 58.5 + - - +
440G VAL* 3.2 25.3 + - - +
520G PHE* 3.9 5.4 - - - +
521G THR* 3.0 44.0 + - - +
531G PO4 2.7 31.2 + - - -
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Residues in contact with ALA 437 (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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429G VAL* 3.7 15.8 - - + +
431G THR* 3.8 22.1 - - + -
434G GLY* 3.0 8.5 + - - +
436G SER* 1.3 73.7 - - - +
438G HIS* 1.3 62.9 + - + +
439G GLN 3.1 1.6 - - - -
440G VAL* 3.3 3.7 + - - +
441G ALA* 3.0 24.4 + - - +
449G ILE* 4.4 3.6 - - + +
451G ALA* 3.8 14.8 - - + -
462G ALA* 6.2 0.4 - - + -
468G ILE* 3.4 24.4 - - + +
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Residues in contact with HIS 438 (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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265G LYS* 5.4 11.2 - - - -
320G GLY 4.9 1.0 - - - +
433G SER 4.7 3.4 - - - -
434G GLY* 3.0 34.9 + - - +
435G ARG* 3.8 10.8 + - - +
437G ALA* 1.3 77.3 - - + +
439G GLN* 1.3 60.7 + - - +
441G ALA* 3.8 2.1 - - - +
442G ARG* 3.2 26.7 + - - +
458G THR* 5.5 1.5 + - + -
461G GLN* 5.5 2.5 - - + -
462G ALA* 4.0 17.3 - - + +
465G TYR* 3.4 60.9 + + + +
468G ILE* 3.6 16.8 - - + -
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Residues in contact with GLN 439 (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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406G ASP* 5.1 1.9 + - - -
408G MET* 3.8 31.4 - - + -
409G GLU* 3.3 32.3 + - + +
412G ALA* 3.3 3.6 - - - +
435G ARG* 3.2 19.1 + - - +
436G SER 4.1 2.2 - - - +
437G ALA 3.1 0.4 - - - -
438G HIS* 1.3 80.5 - - - +
440G VAL* 1.3 62.5 + - - +
442G ARG* 3.2 41.7 - - + +
443G TYR* 3.2 26.7 - - - -
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Residues in contact with VAL 440 (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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408G MET* 4.3 1.8 - - + -
412G ALA* 3.8 16.6 - - + +
415G SER* 5.4 0.2 - - - -
416G VAL* 3.9 12.6 - - + +
427G LEU* 4.0 25.4 - - + -
429G VAL* 3.9 7.9 - - + -
436G SER 3.2 18.4 + - - +
437G ALA 3.3 6.5 + - - +
439G GLN* 1.3 76.6 - - - +
441G ALA* 1.3 65.4 + - - +
443G TYR* 3.1 14.9 + - - +
444G ARG 3.7 0.2 + - - -
445G PRO* 3.4 12.8 - - + +
449G ILE* 4.0 21.1 - - + -
511G LEU* 3.7 26.5 - - + -
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Residues in contact with ALA 441 (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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356G ASP* 5.8 1.1 - - - +
437G ALA 3.0 16.7 + - - +
438G HIS 3.8 5.2 - - - +
439G GLN 3.4 0.2 - - - -
440G VAL* 1.3 78.1 - - - +
442G ARG* 1.3 60.5 + - - +
444G ARG* 3.2 27.6 + - - -
445G PRO* 4.3 1.7 - - - +
449G ILE* 3.5 16.1 - - + +
465G TYR* 4.1 10.5 - - + -
466G ARG* 3.4 24.8 - - - +
468G ILE* 3.8 12.8 - - + -
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Residues in contact with ARG 442 (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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317G ASN* 4.5 5.6 + - - +
318G ARG 2.8 28.3 + - - -
319G ALA* 3.6 18.2 + - - +
320G GLY* 3.8 27.6 - - - +
397G LEU* 3.5 26.9 + - - +
401G SER* 3.7 21.8 + - - -
409G GLU* 3.4 14.8 + - - -
438G HIS 3.2 11.1 + - - +
439G GLN* 3.2 53.7 - - - +
441G ALA* 1.3 75.9 - - - +
443G TYR* 1.3 76.9 + - + +
444G ARG* 3.3 9.9 + - - +
465G TYR* 5.8 0.8 - - + -
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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