Contacts of the strand formed by residues 468 - 472 (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 ILE 468 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B ALA* 3.4 36.3 - - + +
438B HIS* 3.9 8.3 - - + +
441B ALA* 3.9 13.9 - - + -
449B ILE* 3.3 15.9 - - + +
451B ALA* 3.9 22.2 - - + -
462B ALA* 3.7 34.7 - - + +
465B TYR* 3.5 26.2 + - + +
466B ARG 3.2 1.9 - - - +
467B GLY* 1.3 75.6 - - - +
469B PHE* 1.3 62.9 + - - +
470B PRO* 3.3 9.9 - - - +
535B GOL 3.2 22.7 - - - -
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Residues in contact with PHE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 3.8 9.2 - - + -
42B ARG 3.1 36.3 - - - -
43B ASN* 4.0 7.6 - - - -
448B PRO* 3.7 27.6 - - + -
449B ILE 2.6 12.2 + - - +
450B ILE* 3.5 11.6 - - + +
451B ALA 3.2 19.4 + - - -
463B HIS* 6.3 0.2 - + - -
467B GLY 3.5 11.0 - - - -
468B ILE* 1.3 71.4 - - - +
470B PRO* 1.3 67.7 - - + +
471B VAL* 3.5 5.6 + - + +
495B VAL* 6.4 0.9 - - + -
499B ARG* 6.1 1.6 - - - -
501B PHE* 3.5 29.6 - + + -
535B GOL 3.2 31.6 - - - -
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Residues in contact with PRO 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR 4.8 0.5 - - - +
106B PRO* 3.3 21.5 - - + +
451B ALA* 3.6 8.7 - - + +
453B THR* 5.2 1.3 - - + -
459B ALA* 3.2 42.8 - - + +
462B ALA* 3.8 12.3 - - + -
463B HIS* 3.6 35.0 - - + +
468B ILE* 3.3 15.0 - - + +
469B PHE* 1.3 83.6 - - + +
471B VAL* 1.3 61.5 - - - +
535B GOL 5.0 0.2 - - - -
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO 5.3 2.2 - - - +
102B ILE 5.1 1.6 - - - +
104B TYR 5.0 9.6 - - - +
106B PRO* 5.0 0.7 - - - -
450B ILE* 3.8 20.0 - - + -
451B ALA 3.1 11.9 + - - +
452B VAL* 3.7 11.6 - - + -
453B THR* 3.1 30.1 + - - +
459B ALA* 5.1 1.1 - - - -
469B PHE* 4.5 7.2 - - + +
470B PRO* 1.3 78.4 - - - +
472B LEU* 1.3 60.4 + - - +
473B CYS 3.5 1.4 + - - -
491B PHE* 3.8 24.0 - - + -
492B ALA* 5.0 0.4 - - - -
495B VAL* 3.6 35.4 - - + -
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Residues in contact with LEU 472 (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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101B PRO* 4.4 7.3 + - - +
104B TYR* 4.0 37.6 + - + +
106B PRO* 4.9 2.0 - - + +
453B THR 3.3 15.9 - - - +
454B ARG* 3.4 25.1 - - - +
455B ASN 3.9 2.2 - - - +
456B PRO* 3.8 35.2 - - + -
459B ALA* 4.8 7.9 - - + -
470B PRO 4.3 0.6 + - - -
471B VAL* 1.3 70.3 - - - +
473B CYS* 1.3 69.7 - - - +
474B LYS* 3.4 29.9 + - + +
491B PHE* 3.6 12.1 - - - -
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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
------------------------------------------------------------
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