Contacts of the helix formed by residues 455 - 462 (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 ASN 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432B GLU* 3.7 10.1 + - - +
433B SER* 5.8 0.2 - - - +
453B THR* 3.1 18.6 + - - +
454B ARG* 1.3 77.1 - - - +
456B PRO* 1.3 69.5 - - - +
457B GLN* 2.9 25.3 + - - +
458B THR* 3.3 20.7 + - - +
459B ALA* 3.2 16.6 + - - +
472B LEU* 3.9 1.1 - - - -
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Residues in contact with PRO 456 (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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454B ARG 3.4 11.0 - - - +
455B ASN* 1.3 92.1 - - - +
457B GLN* 1.3 55.3 + - - +
459B ALA* 3.3 5.1 + - + +
460B ARG* 2.9 52.5 + - + +
472B LEU* 3.8 27.8 - - + -
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Residues in contact with GLN 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASP* 4.4 15.3 + - - -
236B VAL 4.5 9.7 + - - -
237B ASP* 4.2 11.6 + - - +
263B ASN* 3.4 40.7 + - - +
264B ILE* 4.5 4.6 - - - +
455B ASN* 2.9 12.3 + - - +
456B PRO* 1.3 76.1 - - - +
458B THR* 1.3 60.8 + - - +
460B ARG* 3.8 17.1 - - - +
461B GLN* 2.8 58.4 + - - +
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Residues in contact with THR 458 (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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431B THR* 4.7 4.3 - - + +
432B GLU 2.7 20.9 + - - +
433B SER* 3.6 31.7 + - - +
434B GLY* 3.7 11.7 - - - +
438B HIS* 5.5 1.3 + - - +
453B THR* 3.5 26.0 - - + +
455B ASN* 3.3 14.6 + - - -
457B GLN* 1.3 77.3 - - - +
459B ALA* 1.3 62.2 + - - +
461B GLN* 3.7 6.4 - - - +
462B ALA* 2.9 28.6 + - + +
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Residues in contact with ALA 459 (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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106B PRO* 3.9 24.0 - - + -
453B THR* 3.6 19.9 - - + +
455B ASN 3.2 6.1 + - - +
456B PRO* 3.3 13.0 - - + +
458B THR* 1.3 77.5 - - - +
460B ARG* 1.3 63.7 + - - +
462B ALA* 3.1 10.3 + - - -
463B HIS* 4.3 0.2 - - - -
470B PRO* 3.2 34.3 - - + +
472B LEU* 4.8 10.1 - - + -
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Residues in contact with ARG 460 (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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91B ARG* 5.9 6.5 - - - +
104B TYR* 5.5 7.1 + - - +
106B PRO* 4.1 15.9 - - + -
107B VAL 3.3 23.3 - - - +
108B ALA* 3.3 23.0 - - - +
109B VAL* 5.7 1.1 - - - -
235B ASP* 4.1 19.7 + - - -
237B ASP* 2.7 47.0 + - - +
238B MET* 4.7 0.2 - - - +
456B PRO* 2.9 38.0 + - - +
457B GLN* 3.4 22.7 + - - +
459B ALA* 1.3 75.5 - - - +
461B GLN* 1.3 61.7 + - - +
462B ALA 3.3 0.9 + - - -
463B HIS* 3.3 16.6 + - - +
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Residues in contact with GLN 461 (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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237B ASP* 2.7 38.8 + - + +
238B MET* 4.6 9.6 - - + -
263B ASN* 2.6 32.3 + - - +
264B ILE* 3.9 0.4 - - - +
265B LYS* 3.4 30.5 - - + +
438B HIS* 5.2 4.3 - - + +
457B GLN* 2.8 39.2 + - + +
458B THR* 3.7 5.6 + - - +
460B ARG* 1.3 67.2 - - - +
462B ALA* 1.3 58.2 + - - +
463B HIS 3.1 6.6 + - - -
464B LEU* 3.5 21.3 + - + +
465B TYR* 3.9 9.5 - - + -
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Residues in contact with ALA 462 (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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434B GLY* 6.3 0.4 - - - -
437B ALA* 6.1 1.1 - - + -
438B HIS* 4.6 9.4 - - - +
451B ALA* 5.4 3.4 - - + -
453B THR* 6.2 0.4 - - + -
458B THR* 2.9 22.3 + - + +
459B ALA 3.1 10.4 + - - +
461B GLN* 1.3 76.6 - - - +
463B HIS* 1.3 62.9 + - - +
464B LEU 3.2 0.7 - - - -
465B TYR* 3.3 25.2 + - - +
468B ILE* 3.7 33.8 - - + +
470B PRO* 3.8 10.1 - - + -
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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