Contacts of the helix formed by residues 455 - 462 (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 ASN 455 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432G GLU* 3.7 10.9 + - - +
433G SER* 5.9 0.4 - - - +
453G THR* 2.8 19.9 + - - +
454G ARG* 1.3 79.6 - - - +
456G PRO* 1.3 68.2 - - - +
457G GLN* 3.0 23.2 + - - +
458G THR* 3.3 20.1 + - - +
459G ALA 3.2 16.1 + - - -
472G LEU* 3.6 2.5 - - - +
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Residues in contact with PRO 456 (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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454G ARG 3.4 7.9 - - - +
455G ASN* 1.3 87.4 - - - +
457G GLN* 1.3 57.8 + - - +
459G ALA* 3.2 4.1 + - + +
460G ARG* 2.9 52.9 + - - +
472G LEU* 3.7 31.4 - - + -
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Residues in contact with GLN 457 (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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235G ASP* 5.0 8.1 + - - +
236G VAL 4.7 4.6 + - - -
237G ASP* 4.0 11.4 + - - +
263G ASN* 3.1 51.1 + - - +
264G ILE* 4.0 12.5 - - - +
455G ASN* 3.0 10.8 + - - +
456G PRO* 1.3 75.3 - - - +
458G THR* 1.3 60.7 + - - +
460G ARG* 3.8 17.0 - - - +
461G GLN* 2.9 49.7 + - - +
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Residues in contact with THR 458 (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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431G THR* 4.5 4.3 - - + +
432G GLU 3.2 19.0 + - - +
433G SER* 3.4 32.4 + - - +
434G GLY* 3.8 11.4 - - - +
438G HIS* 5.5 1.7 + - + +
453G THR* 3.9 15.9 - - + +
455G ASN* 3.3 21.6 + - - -
457G GLN* 1.3 74.6 - - - +
459G ALA* 1.3 66.3 + - - +
461G GLN* 3.2 5.7 + - - -
462G ALA* 2.9 32.1 + - + +
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Residues in contact with ALA 459 (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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106G PRO* 4.1 22.2 - - + -
453G THR* 3.9 14.1 - - + +
455G ASN 3.2 9.4 + - - +
456G PRO* 3.2 13.2 + - + +
458G THR* 1.3 78.8 - - - +
460G ARG* 1.3 62.4 + - - +
462G ALA* 3.7 1.6 + - - -
463G HIS* 3.3 4.2 + - - -
470G PRO* 3.2 36.8 - - + +
472G LEU* 4.4 14.1 - - + +
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Residues in contact with ARG 460 (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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91G ARG* 5.6 7.4 - - - +
104G TYR* 6.0 1.8 - - - +
106G PRO* 4.4 11.0 - - + -
107G VAL 3.1 28.5 - - - +
108G ALA* 3.6 14.9 - - - +
109G VAL* 5.8 1.1 - - - -
235G ASP* 4.1 22.4 + - - -
237G ASP* 2.7 43.8 + - - +
238G MET* 4.5 0.3 - - - +
456G PRO* 2.9 43.7 + - + +
457G GLN* 3.8 18.9 - - - +
459G ALA* 1.3 76.6 - - - +
461G GLN* 1.3 60.6 + - - +
463G HIS* 3.1 28.0 + - - +
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Residues in contact with GLN 461 (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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237G ASP* 2.6 42.0 + - + +
238G MET* 3.9 11.7 - - + -
263G ASN* 2.7 28.9 + - - +
264G ILE* 3.6 1.0 - - - +
265G LYS* 3.3 33.5 - - + +
438G HIS* 5.1 3.8 - - + +
457G GLN* 2.9 39.8 + - - +
458G THR* 4.1 4.3 + - - +
460G ARG* 1.3 70.2 - - - +
462G ALA* 1.3 62.5 + - - +
463G HIS 3.2 1.0 + - - -
464G LEU* 3.4 24.4 + - - +
465G TYR* 4.2 4.9 - - - -
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Residues in contact with ALA 462 (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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437G ALA* 6.2 0.4 - - + -
438G HIS* 4.0 21.1 - - - +
451G ALA* 5.5 2.5 - - + -
458G THR* 2.9 20.8 + - + +
459G ALA* 3.8 8.7 - - - +
460G ARG 3.2 0.4 - - - -
461G GLN* 1.3 72.9 - - - +
463G HIS* 1.3 56.2 + - - +
464G LEU 3.0 5.4 - - - -
465G TYR* 3.0 30.3 + - - +
468G ILE* 3.8 19.7 - - + +
470G PRO* 3.8 15.7 - - + -
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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