Contacts of the strand formed by residues 449 - 453 (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 ILE 449 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G LEU* 3.4 15.5 - - + +
429G VAL* 3.8 24.5 - - + -
437G ALA* 4.4 6.7 - - + +
440G VAL* 4.0 9.4 - - + -
441G ALA* 3.5 43.1 - - + +
445G PRO* 3.8 24.5 - - + -
447G ALA 4.4 0.4 - - - +
448G PRO* 1.3 72.6 - - - +
450G ILE* 1.3 63.9 + - - +
451G ALA 4.5 1.8 - - - +
466G ARG 4.0 7.2 - - - +
467G GLY* 2.8 14.1 + - - +
468G ILE* 3.5 16.7 - - + -
469G PHE* 2.5 35.9 + - - +
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Residues in contact with ILE 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G ALA* 4.0 14.4 - - + -
427G LEU 2.8 12.0 + - - +
428G ILE* 3.5 11.3 - - + -
429G VAL 3.0 24.6 + - - +
448G PRO* 3.8 3.1 + - + +
449G ILE* 1.3 73.2 - - - +
451G ALA* 1.3 59.2 + - - +
452G VAL* 3.6 2.9 + - - +
469G PHE* 3.3 15.0 - - + +
471G VAL* 3.7 30.7 - - + -
492G ALA* 4.0 27.6 - - + +
495G VAL* 4.7 4.9 - - + -
496G GLY* 4.4 3.4 - - - +
501G PHE* 4.4 17.9 - - + -
502G PHE* 3.7 29.8 - - + -
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Residues in contact with ALA 451 (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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429G VAL* 3.4 7.2 - - - -
431G THR* 3.9 9.2 - - + -
437G ALA* 3.8 21.3 - - + -
449G ILE* 3.7 2.3 + - + -
450G ILE* 1.3 69.0 - - - +
452G VAL* 1.3 63.4 + - - +
453G THR* 3.8 4.9 + - + +
462G ALA* 5.5 2.5 - - + -
468G ILE* 3.7 26.2 - - + -
469G PHE 3.0 9.8 + - - +
470G PRO* 3.4 5.7 - - + +
471G VAL* 2.9 26.2 + - - +
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Residues in contact with VAL 452 (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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428G ILE* 4.4 0.7 - - + -
429G VAL 2.9 7.2 + - - +
430G LEU* 3.9 17.1 - - + +
431G THR 3.2 25.8 + - - +
450G ILE 4.0 7.6 - - - +
451G ALA* 1.3 69.9 - - - +
453G THR* 1.3 63.7 + - - +
471G VAL* 3.7 14.1 - - + +
473G CYS* 4.1 5.4 - - + -
488G ARG* 3.6 41.3 + - + +
491G PHE* 3.9 19.1 - - + -
492G ALA* 3.5 31.4 - - + -
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Residues in contact with THR 453 (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* 3.2 24.5 + - + -
432G GLU* 3.7 5.6 + - - +
451G ALA* 4.3 7.2 - - + +
452G VAL* 1.3 73.8 - - - +
454G ARG* 1.3 54.5 + - - +
455G ASN* 2.8 45.5 + - - +
458G THR* 3.9 7.6 - - + -
459G ALA* 3.9 25.6 - - + +
470G PRO* 5.4 0.7 - - + -
471G VAL 3.2 9.9 + - - +
472G LEU* 3.4 4.5 - - - +
473G CYS* 2.7 32.4 + - - -
488G ARG* 5.6 3.4 - - - +
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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