Contacts of the strand formed by residues 628 - 634 (chain B) in PDB entry 3QFR
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 HIS 628 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522B ARG 4.6 2.2 - - - -
523B LEU 5.0 0.2 - - - -
524B PRO* 3.6 37.7 - - + +
529B THR* 3.7 11.9 - - + +
530B PRO 3.2 6.0 + - - +
531B VAL* 3.8 0.4 - - + -
532B ILE* 2.9 28.6 + - - +
626B GLY 4.0 1.1 + - - -
627B ALA* 1.3 72.6 - - - +
629B ILE* 1.3 58.9 + - - +
630B TYR* 3.2 36.2 - + + -
671B LYS 5.5 0.4 + - - -
672B GLY 3.3 24.5 + - - -
673B ARG* 3.0 30.0 - - + +
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Residues in contact with ILE 629 (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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532B ILE* 3.4 18.6 - - + +
534B VAL* 5.2 0.9 - - + -
623B ILE* 3.5 33.2 - - + -
627B ALA 4.4 7.2 - - - +
628B HIS* 1.3 75.4 - - - +
630B TYR* 1.3 73.2 + - - +
631B VAL* 4.5 1.3 - - + -
646B PHE* 3.3 40.6 - - + -
665B ILE* 5.3 0.9 - - + -
668B LEU* 4.5 9.2 - - + -
673B ARG 2.6 11.8 + - - +
674B TYR* 3.2 34.0 - - + -
675B SER 2.9 25.8 + - - +
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Residues in contact with TYR 630 (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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521B PHE* 3.4 25.8 - + + -
522B ARG 2.3 37.5 + - - -
523B LEU* 3.5 7.0 - - - -
524B PRO* 3.6 1.0 - - - +
531B VAL* 3.8 14.4 - - + -
532B ILE 2.6 23.5 + - - +
533B MET* 3.5 6.9 - - + -
534B VAL* 2.6 36.6 + - - +
543B PHE* 3.5 20.6 - - + -
546B PHE* 3.6 16.2 - + - -
628B HIS* 3.2 46.7 - + + +
629B ILE* 1.3 76.0 - - - +
631B VAL* 1.3 60.6 + - - +
673B ARG 6.1 0.4 - - - -
675B SER* 3.5 20.0 - - - -
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Residues in contact with VAL 631 (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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521B PHE* 4.4 1.4 - - - -
534B VAL* 3.3 10.3 - - + +
543B PHE* 4.6 0.4 - - - -
629B ILE* 4.5 6.1 - - + -
630B TYR* 1.3 78.7 - - - +
632B CYS* 1.3 60.6 + - - +
638B MET* 3.9 28.3 - - + -
639B ALA* 4.1 20.0 - - + +
642B VAL* 3.9 24.9 - - + -
674B TYR* 4.0 21.3 - - + +
675B SER 3.1 6.3 + - - +
676B LEU* 3.4 18.7 - - + +
677B ASP* 3.0 24.8 + - - +
678B VAL* 4.3 1.8 - - + +
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Residues in contact with CYS 632 (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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521B PHE* 4.9 0.7 - - + -
534B VAL 2.9 6.9 + - - +
535B GLY* 3.5 15.6 - - - -
536B PRO* 3.9 0.5 - - - +
539B GLY* 2.9 31.3 - - - +
542B PRO* 3.3 24.7 - - + -
543B PHE* 3.8 16.1 - - + -
631B VAL* 1.3 73.9 - - - +
633B GLY* 1.3 68.7 + - - +
638B MET* 3.2 15.7 - - - +
677B ASP* 3.1 27.1 - - + +
678B VAL* 4.5 1.1 - - - -
679B TRP* 3.5 10.5 - - - -
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Residues in contact with GLY 633 (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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536B PRO 5.0 2.5 - - - -
539B GLY* 3.8 16.4 - - - -
632B CYS* 1.3 78.8 - - - +
634B ASP* 1.3 62.8 + - - -
638B MET* 3.7 2.2 - - - -
677B ASP 3.0 9.1 + - - -
678B VAL* 3.1 4.8 - - - -
679B TRP* 3.0 44.9 + - - +
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Residues in contact with ASP 634 (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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633B GLY* 1.3 68.9 - - - -
635B ALA* 1.3 62.9 + - - +
636B ARG* 3.2 18.1 + - - +
637B ASN* 3.4 17.4 + - - +
638B MET* 3.1 35.8 + - + +
639B ALA* 3.0 26.5 + - - +
678B VAL* 4.3 0.4 - - - -
679B TRP* 4.0 8.1 - - - +
680B SER* 5.5 1.4 - - - -
753B NAP 5.1 8.0 + - - +
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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