Contacts of the helix formed by residues 434 - 442 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B THR* 2.8 20.2 + - - -
432B GLU 3.6 0.8 - - - -
433B SER* 1.3 77.8 - - - +
435B ARG* 1.3 54.7 + - - +
436B SER 3.2 3.1 - - - -
437B ALA* 2.9 6.5 + - - +
438B HIS* 2.8 51.6 + - - -
458B THR* 3.7 12.3 - - - +
462B ALA* 6.3 0.7 - - - -
531B PO4 3.2 0.4 + - - -
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Residues in contact with ARG 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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408B MET* 4.6 2.8 - - + +
433B SER* 2.4 41.7 + - - +
434B GLY* 1.3 75.4 - - - +
436B SER* 1.3 55.6 + - - +
438B HIS* 3.5 15.0 + - + +
439B GLN* 3.1 34.8 + - - +
519B GLY* 2.7 28.9 + - - -
520B PHE* 5.3 1.0 - - - +
531B PO4 2.8 21.4 + - - +
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET* 3.3 30.9 - - - +
429B VAL* 4.2 8.5 - - - -
431B THR* 4.4 2.0 - - - -
435B ARG* 1.3 76.2 - - - +
437B ALA* 1.3 61.8 + - - +
440B VAL* 3.4 15.9 + - - +
520B PHE* 3.7 2.1 - - - +
521B THR* 3.1 44.7 + - - -
531B PO4 3.0 28.4 + - - -
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B VAL* 4.0 13.1 - - + +
431B THR* 4.0 10.7 + - + -
434B GLY* 2.9 10.1 + - - +
436B SER* 1.3 74.2 - - - +
438B HIS* 1.3 66.7 + - + +
439B GLN 3.1 1.7 + - - -
440B VAL* 3.3 5.6 + - - +
441B ALA 3.0 18.5 + - - -
449B ILE* 4.8 2.8 - - + +
451B ALA* 3.8 26.5 - - + -
462B ALA* 6.1 0.9 - - + -
468B ILE* 3.4 26.2 - - + +
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Residues in contact with HIS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 5.6 10.5 - - - -
320B GLY 4.9 2.5 - - - +
433B SER 4.0 7.0 - - - -
434B GLY* 2.8 45.0 + - - +
435B ARG* 3.7 15.1 + - + +
437B ALA* 1.3 72.3 - - + +
439B GLN* 1.3 64.8 + - - +
441B ALA* 3.6 2.9 + - - +
442B ARG* 3.3 22.7 + - - +
458B THR 5.5 1.4 + - - -
461B GLN* 4.8 4.1 + - + -
462B ALA* 4.6 12.0 + - + +
465B TYR* 3.4 67.1 + + + -
468B ILE* 4.0 10.1 - - + -
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ASP* 5.1 2.0 - - - -
408B MET* 3.8 27.6 - - + -
409B GLU* 3.5 27.5 + - + +
412B ALA* 3.3 13.3 - - - +
435B ARG* 3.1 22.2 + - - +
436B SER 3.7 6.1 - - - +
437B ALA 3.1 0.2 - - - -
438B HIS* 1.3 80.5 - - - +
440B VAL* 1.3 62.1 + - - +
442B ARG* 3.0 63.3 - - - +
443B TYR* 3.5 2.4 - - - -
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Residues in contact with VAL 440 (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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408B MET* 4.1 10.1 - - + -
412B ALA* 3.8 13.5 - - + -
415B SER* 5.2 0.4 - - - -
416B VAL* 3.7 21.3 - - + +
427B LEU* 4.1 19.1 - - + -
429B VAL* 4.4 6.7 - - + -
436B SER 3.4 15.0 + - - +
437B ALA* 3.3 7.7 + - - +
439B GLN* 1.3 73.8 - - - +
441B ALA* 1.3 65.0 + - - +
442B ARG 3.3 0.7 + - - -
443B TYR 3.4 7.3 + - - -
444B ARG 3.7 0.2 + - - -
445B PRO* 3.3 14.6 - - + +
449B ILE* 4.2 21.8 - - + -
511B LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 441 (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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437B ALA 3.0 17.1 + - - +
438B HIS 3.6 7.0 - - - +
439B GLN 3.3 0.2 - - - -
440B VAL* 1.3 77.7 - - - +
442B ARG* 1.3 56.4 + - - +
444B ARG* 3.0 34.3 + - - -
445B PRO* 4.3 1.0 - - - +
449B ILE* 3.7 11.4 - - - +
465B TYR* 4.2 11.0 - - + -
466B ARG 3.4 22.4 - - - +
468B ILE* 3.9 16.4 - - + -
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Residues in contact with ARG 442 (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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317B ASN* 4.4 7.8 + - - +
318B ARG 2.7 29.3 + - - -
319B ALA* 3.3 22.0 + - - +
320B GLY* 3.7 25.6 - - - +
397B LEU* 3.3 23.7 - - - +
401B SER* 4.3 14.1 - - - -
409B GLU* 3.4 17.6 + - - -
438B HIS 3.3 10.0 + - - +
439B GLN* 3.0 49.8 - - - +
440B VAL 3.2 1.4 - - - -
441B ALA* 1.3 78.6 - - - +
443B TYR* 1.3 81.3 + - + +
444B ARG* 3.2 11.5 + - - +
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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