Contacts of the helix formed by residues 434 - 442 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A THR* 2.9 22.3 + - - -
432A GLU 3.4 1.6 - - - -
433A SER* 1.3 77.4 - - - +
435A ARG* 1.3 64.2 + - - +
437A ALA* 2.9 15.5 + - - +
438A HIS* 2.9 31.0 + - - -
458A THR* 3.6 13.6 - - - +
462A ALA* 6.2 1.1 - - - -
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Residues in contact with ARG 435 (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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408A MET* 5.2 2.5 - - + -
433A SER* 2.8 33.3 + - - +
434A GLY* 1.3 74.5 - - - +
436A SER* 1.3 63.7 + - - +
438A HIS* 3.0 27.7 + - + +
439A GLN* 3.1 18.1 + - - +
519A GLY* 3.2 21.6 + - - -
520A PHE* 4.9 4.4 - - - +
531A PO4 2.7 26.9 + - - +
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Residues in contact with SER 436 (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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408A MET* 3.2 35.4 - - - +
429A VAL* 4.3 6.1 - - - -
431A THR* 4.3 0.4 - - - -
435A ARG* 1.3 77.5 - - - +
437A ALA* 1.3 59.5 + - - +
439A GLN 3.6 0.2 + - - -
440A VAL* 3.3 14.2 + - - +
520A PHE* 3.7 2.8 - - - +
521A THR* 3.0 44.5 + - - +
531A PO4 2.7 30.0 + - - -
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Residues in contact with ALA 437 (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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429A VAL* 3.8 24.0 - - + +
431A THR* 4.0 14.1 + - + -
434A GLY* 2.9 10.5 + - - +
436A SER* 1.3 75.0 - - - +
438A HIS* 1.3 65.7 + - + +
440A VAL* 3.3 7.4 + - - +
441A ALA* 3.0 23.2 + - - +
449A ILE* 4.7 3.9 - - + +
451A ALA* 4.2 11.4 - - + -
462A ALA* 6.3 0.4 - - + -
468A ILE* 3.6 20.5 - - + +
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Residues in contact with HIS 438 (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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265A LYS* 4.6 14.1 - - - -
320A GLY 5.3 2.3 - - - +
433A SER 4.3 5.2 - - - -
434A GLY* 2.9 38.1 + - - -
435A ARG* 3.0 15.5 + - + +
437A ALA* 1.3 75.8 - - + +
439A GLN* 1.3 62.5 + - - +
441A ALA* 3.3 2.6 + - - +
442A ARG* 2.9 30.0 + - - +
458A THR 5.8 0.4 + - - -
461A GLN* 5.2 2.2 + - + +
462A ALA* 4.7 9.7 + - - +
465A TYR* 3.3 64.5 + + + -
468A ILE* 3.9 12.6 - - + -
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Residues in contact with GLN 439 (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 ASP* 5.2 2.7 - - - -
408A MET* 3.7 38.4 - - + +
409A GLU* 3.4 32.1 + - + +
412A ALA* 3.3 2.9 - - + +
435A ARG* 3.1 13.7 + - - +
436A SER 3.8 0.9 - - - +
437A ALA 3.2 0.2 - - - -
438A HIS* 1.3 79.9 - - - +
440A VAL* 1.3 61.4 + - - +
442A ARG* 2.9 47.9 - - - +
443A TYR* 3.1 29.3 - - - -
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Residues in contact with VAL 440 (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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408A MET* 4.2 6.1 - - + -
412A ALA* 4.0 11.9 - - + +
415A SER* 5.3 0.2 - - - -
416A VAL* 3.8 19.5 - - + +
427A LEU* 4.0 17.9 - - + -
429A VAL* 4.1 8.5 - - + -
436A SER 3.3 16.8 - - - +
437A ALA* 3.3 6.3 + - - +
439A GLN* 1.3 75.2 - - - +
441A ALA* 1.3 64.6 + - - +
443A TYR* 3.1 13.2 + - - -
444A ARG 3.6 0.2 + - - -
445A PRO* 3.4 11.9 - - + +
449A ILE* 3.7 25.6 - - + -
511A LEU* 3.5 27.6 - - + -
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Residues in contact with ALA 441 (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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437A ALA 3.0 17.1 + - - +
438A HIS 3.3 5.8 + - - +
440A VAL* 1.3 77.4 - - - +
442A ARG* 1.3 55.9 + - - +
444A ARG* 2.9 36.9 + - - +
445A PRO* 4.3 0.8 - - - +
449A ILE* 3.7 10.5 - - + +
465A TYR* 4.1 10.8 - - + -
466A ARG 3.5 22.0 - - - +
468A ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 442 (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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317A ASN 4.4 5.5 + - - +
318A ARG 2.6 30.0 + - - -
319A ALA* 4.0 16.5 + - - +
320A GLY* 3.9 23.3 - - - +
397A LEU* 3.3 27.0 + - - +
401A SER* 3.9 19.8 - - - -
409A GLU* 3.8 13.5 + - - -
438A HIS 2.9 11.9 + - - +
439A GLN* 2.9 55.1 - - - +
440A VAL 3.2 0.8 - - - -
441A ALA* 1.3 76.2 - - - +
443A TYR* 1.3 79.8 + - + +
444A ARG* 3.3 14.9 + - - +
465A TYR* 5.9 0.9 - - + -
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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