Contacts of the helix formed by residues 434 - 442 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431D THR* 2.9 18.0 + - - -
432D GLU 3.4 1.0 - - - -
433D SER* 1.3 79.4 + - - +
435D ARG* 1.3 63.6 + - - +
436D SER 3.3 2.9 - - - -
437D ALA* 3.0 14.3 + - - +
438D HIS* 3.1 33.8 + - - -
458D THR* 3.7 12.8 - - - +
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Residues in contact with ARG 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D MET* 4.9 2.6 - - + +
433D SER* 2.7 44.4 + - - +
434D GLY* 1.3 75.7 - - - +
436D SER* 1.3 60.5 + - - +
437D ALA 3.2 1.2 + - - -
438D HIS* 3.3 11.9 + - + +
439D GLN* 3.2 28.5 + - - +
519D GLY* 3.3 22.4 + - - -
520D PHE* 5.7 0.2 - - - +
531D PO4 3.1 9.8 + - - +
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Residues in contact with SER 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D MET* 3.3 28.0 - - - +
429D VAL* 3.5 16.1 - - - +
431D THR* 4.3 0.4 - - - -
435D ARG* 1.3 76.0 - - - +
437D ALA* 1.3 58.2 + - - +
439D GLN 4.4 0.4 - - - -
440D VAL* 3.7 7.4 - - - +
520D PHE* 3.5 9.9 - - - +
521D THR* 3.1 37.7 + - - +
531D PO4 3.0 32.7 + - - -
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Residues in contact with ALA 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429D VAL* 4.1 13.2 - - + +
431D THR* 4.0 21.9 + - + -
434D GLY* 3.0 9.6 + - - +
436D SER* 1.3 76.7 - - - +
438D HIS* 1.3 66.9 + - + +
439D GLN 3.2 1.8 - - - -
440D VAL* 3.4 4.8 + - - +
441D ALA* 3.1 18.2 + - - +
449D ILE* 4.6 2.1 - - + +
451D ALA* 4.1 14.8 - - + -
462D ALA* 6.3 0.4 - - + -
468D ILE* 3.4 25.6 - - + +
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Residues in contact with HIS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LYS* 4.6 16.5 + - - -
320D GLY 4.9 1.5 - - - +
433D SER 4.9 2.9 - - - -
434D GLY* 3.1 34.2 + - - -
435D ARG* 3.3 12.5 + - + +
437D ALA* 1.3 77.6 - - + +
439D GLN* 1.3 63.5 + - - +
441D ALA* 3.5 3.7 - - - +
442D ARG* 3.2 26.3 + - - +
458D THR* 5.5 1.6 + - + +
461D GLN* 4.8 4.6 + - + +
462D ALA* 4.4 13.9 + - + +
465D TYR* 3.3 63.0 + + + +
468D ILE* 3.6 17.3 - - + -
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Residues in contact with GLN 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D GLY 5.6 1.6 - - - +
406D ASP* 4.7 4.0 + - - +
408D MET* 4.0 29.6 - - + -
409D GLU* 3.4 31.7 + - + +
412D ALA* 3.4 2.8 - - + +
435D ARG* 3.2 16.1 + - - +
437D ALA 3.2 1.0 - - - -
438D HIS* 1.3 83.8 - - - +
440D VAL* 1.3 60.8 + - - +
442D ARG* 3.0 44.9 - - - +
443D TYR* 3.0 28.6 - - + -
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Residues in contact with VAL 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D MET* 4.2 1.6 - - + -
412D ALA* 3.8 20.9 - - + +
415D SER* 5.0 0.2 - - - -
416D VAL* 3.8 10.0 - - + +
427D LEU* 3.8 26.7 - - + -
429D VAL* 4.3 5.4 - - + -
436D SER 3.7 17.5 - - - +
437D ALA 3.4 8.3 + - - +
439D GLN* 1.3 76.0 - - - +
441D ALA* 1.3 65.8 + - - +
443D TYR* 3.1 15.4 + - - +
444D ARG 3.7 0.2 + - - -
445D PRO* 3.4 11.3 - - + +
449D ILE* 3.8 20.9 - - + -
511D LEU* 3.7 26.5 - - + -
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Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437D ALA 3.1 12.0 + - - +
438D HIS 3.5 11.0 - - - +
440D VAL* 1.3 79.0 - - - +
442D ARG* 1.3 56.4 + - - +
444D ARG* 2.9 35.8 + - - -
445D PRO* 4.0 1.0 - - - +
449D ILE* 3.7 14.5 - - + +
465D TYR* 4.1 20.4 - - + -
466D ARG 3.2 23.7 - - - +
468D ILE* 4.1 2.7 - - + -
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Residues in contact with ARG 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D ASN* 4.4 7.5 + - - +
318D ARG 2.8 28.3 + - - -
319D ALA* 3.0 19.8 + - - +
320D GLY* 3.5 25.1 - - - +
397D LEU* 3.3 26.9 + - - +
401D SER* 4.2 14.1 - - - -
409D GLU* 3.3 20.4 + - - -
438D HIS 3.2 9.5 + - - +
439D GLN* 3.0 55.0 - - - +
440D VAL 3.2 0.6 - - - -
441D ALA* 1.3 77.5 - - - +
443D TYR* 1.3 77.7 + - + +
444D ARG* 3.3 11.1 + - - +
465D TYR* 5.8 1.1 - - + -
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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