Contacts of the strand formed by residues 666 - 675 (chain A) in PDB entry 1QFG
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 TYR 666 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY* 4.7 8.5 + - - -
80A THR* 5.4 0.5 + - - -
648A ARG 4.9 2.9 - - - -
649A TYR* 3.4 2.1 - - - -
650A THR* 2.7 83.3 + - + +
663A VAL* 5.3 0.7 - - + -
664A GLY 3.5 20.4 - - - -
665A SER* 1.3 74.2 + - - +
667A THR* 1.3 68.3 + - - +
668A VAL* 5.1 4.5 - - + -
697A ARG* 3.9 15.7 - - - +
699A TYR* 3.2 55.7 - + + -
700A VAL 3.4 8.7 - - - -
701A ALA* 2.7 37.1 + - - +
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Residues in contact with THR 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A GLY* 5.1 0.9 - - - -
648A ARG 3.1 14.8 - - - +
649A TYR* 3.1 27.7 - - - -
666A TYR* 1.3 73.1 - - - +
668A VAL* 1.3 70.8 + - - +
669A VAL* 4.9 10.8 - - + +
695A PHE* 5.7 3.6 - - - -
697A ARG* 3.3 29.5 + - - +
1102A DDQ 4.1 22.3 - - + +
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Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A GLY 3.9 0.2 - - - +
647A GLY* 3.4 2.6 - - - -
648A ARG* 2.8 63.7 + - - +
666A TYR* 5.1 4.7 - - + -
667A THR* 1.3 80.0 - - - +
669A VAL* 1.3 69.3 - - - +
670A ASP* 4.2 1.0 + - - +
692A ASN* 5.8 0.2 - - + -
693A ASN* 3.4 40.2 - - + +
697A ARG* 5.2 2.7 - - + -
699A TYR* 3.7 42.6 - - + +
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Residues in contact with VAL 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A THR* 4.2 6.7 - - - +
646A GLY 3.2 11.9 - - - +
647A GLY* 4.5 5.2 - - - -
667A THR* 4.2 10.7 + - + +
668A VAL* 1.3 80.7 - - - +
670A ASP* 1.3 67.3 + - - +
693A ASN* 3.0 6.4 + - - +
694A LEU* 2.7 63.1 + - + +
695A PHE* 4.0 32.1 - - + +
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Residues in contact with ASP 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TYR* 4.5 7.1 + - - +
628A TRP* 5.7 3.1 - - - +
645A THR* 3.0 6.0 + - - -
646A GLY 2.6 37.6 + - - +
648A ARG* 2.4 44.5 + - - -
668A VAL* 4.2 0.3 - - - +
669A VAL* 1.3 76.6 - - - +
671A ALA* 1.3 61.0 + - - +
691A VAL 3.5 3.4 - - - -
692A ASN* 2.8 48.2 - - - +
693A ASN 3.0 5.2 + - - -
694A LEU* 5.0 0.4 - - - -
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Residues in contact with ALA 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A TRP* 5.8 1.6 - - - +
644A GLY 3.2 15.3 - - - +
645A THR* 3.6 12.1 - - - +
670A ASP* 1.3 77.3 - - - +
672A LEU* 1.3 65.2 + - - +
673A VAL* 6.3 0.4 - - + -
690A HIS* 3.6 1.2 - - - +
691A VAL* 2.8 43.7 + - + +
694A LEU* 4.6 15.0 - - + +
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Residues in contact with LEU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.3 53.6 - - + +
61A HIS* 4.4 7.9 - - + -
628A TRP* 4.4 11.4 - - + +
642A THR* 4.4 7.2 - - + +
643A LEU* 3.5 0.5 - - - +
644A GLY* 2.9 45.9 + - - +
671A ALA* 1.3 77.6 - - - +
673A VAL* 1.3 76.9 + - - +
674A ARG* 4.1 14.1 - - + +
688A ALA* 5.9 0.2 - - + -
689A LEU 3.2 13.0 - - - +
690A HIS* 3.6 19.7 - - + +
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Residues in contact with VAL 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LEU* 5.3 6.1 - - + -
642A THR 3.2 6.1 - - - -
643A LEU* 3.1 31.0 - - + -
671A ALA* 6.3 0.2 - - + -
672A LEU* 1.3 78.2 - - - +
674A ARG* 1.3 60.5 + - - +
688A ALA* 3.4 1.9 - - - +
689A LEU* 2.7 64.7 + - + +
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Residues in contact with ARG 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TRP* 4.1 33.0 - - - -
59A ALA* 3.6 31.5 + - - +
60A LEU* 3.9 19.9 + - - +
640A GLY 3.7 0.7 - - - +
641A LEU* 3.3 6.8 - - - +
642A THR* 2.6 46.8 + - - +
672A LEU* 4.1 9.4 - - + -
673A VAL* 1.3 76.0 - - - +
675A TYR* 1.3 64.1 + - - +
676A ASP* 5.4 5.1 - - - +
686A ASN* 3.0 45.2 + - + +
687A VAL 3.5 11.0 - - - +
688A ALA* 4.0 12.2 - - + +
722A THR* 5.8 0.8 - - - +
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Residues in contact with TYR 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A PRO 5.3 5.2 + - - -
638A LEU* 5.6 1.1 - - - -
639A SER 3.4 21.0 + - - -
640A GLY 3.2 12.3 - - - -
641A LEU* 4.2 16.2 - - + -
674A ARG* 1.3 71.5 - - - +
676A ASP* 1.3 53.2 + - - +
677A LEU* 2.6 41.1 + - + -
679A ARG* 3.2 37.5 + - + +
680A VAL* 5.0 10.9 - - + +
686A ASN* 3.4 3.2 - - - -
687A VAL* 2.9 37.5 + - + +
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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