Contacts of the strand formed by residues 667 - 676 (chain A) in PDB entry 1LQF
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 GLU 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A TRP* 3.1 25.7 - - + -
661A GLU* 3.3 0.9 - - - -
662A ASN 2.8 26.5 + - - -
665A THR* 3.1 20.7 + - - +
666A GLN* 1.3 77.9 - - - +
668A THR* 1.3 66.6 + - - +
669A ARG* 3.3 28.3 + - - +
562C GLU* 4.1 20.5 - - - +
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Residues in contact with THR 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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659A GLU* 2.7 32.7 + - + +
660A LEU 3.3 3.4 - - - +
661A GLU* 3.2 41.3 - - + +
666A GLN 3.8 4.3 + - - +
667A GLU* 1.3 77.4 - - - +
669A ARG* 1.3 67.3 + - - +
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Residues in contact with ARG 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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599A VAL 4.4 0.2 + - - -
600A TRP* 2.7 66.1 + - + +
603A LYS* 3.4 46.9 - - - +
604A SER 5.3 7.1 + - - -
659A GLU* 3.6 8.0 - - - -
660A LEU* 2.9 35.3 + - + +
667A GLU* 3.3 23.4 + - - +
668A THR* 1.3 81.7 - - - +
670A GLU* 1.3 66.6 + - - +
671A ILE* 3.7 10.8 + - + -
562C GLU* 4.2 4.0 + - - -
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Residues in contact with GLU 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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605A ARG* 3.2 48.9 + - - +
657A GLN* 2.5 45.9 + - + +
658A LEU 3.4 12.1 - - - +
659A GLU* 4.1 10.5 + - - +
669A ARG* 1.3 76.0 - - - +
671A ILE* 1.3 67.3 + - - +
672A LEU* 4.1 7.6 - - - +
707D GLU* 5.6 1.2 - - - +
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Residues in contact with ILE 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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596A TRP* 4.1 13.0 - - + -
599A VAL* 3.7 16.4 - - + -
604A SER 3.3 25.6 - - - +
605A ARG 3.2 9.9 - - - +
607A VAL* 4.0 26.5 - - + -
642A LEU* 5.8 0.2 - - + -
657A GLN 3.9 0.3 - - - -
658A LEU* 3.0 45.0 + - + +
660A LEU* 4.0 31.4 - - + -
669A ARG* 4.2 11.7 - - + +
670A GLU* 1.3 81.0 - - - +
672A LEU* 1.3 70.3 + - - +
673A HIS 3.9 0.5 + - - -
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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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605A ARG* 2.9 49.9 + - - +
606A GLY* 3.2 1.9 - - - -
607A VAL* 2.8 27.7 + - - +
655A VAL* 5.4 5.6 - - + -
656A ARG 4.1 6.7 - - - +
657A GLN* 4.0 23.1 - - + -
670A GLU* 4.1 9.2 - - - +
671A ILE* 1.3 82.1 - - - +
673A HIS* 1.3 59.3 + - - +
674A PHE* 3.5 21.0 - - + -
701A SER* 3.9 22.2 - - - -
703A SER* 4.0 1.8 - - - +
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Residues in contact with HIS 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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596A TRP* 5.1 1.1 - + - -
607A VAL* 3.5 23.8 - - + -
609A MET* 4.2 15.4 - - + +
624A TYR* 2.9 37.9 + + - -
625A TRP* 4.3 13.7 - + - -
654A THR 3.4 6.6 - - - +
655A VAL* 3.4 1.9 - - - +
656A ARG* 2.9 68.6 + - + +
658A LEU* 3.8 28.0 - - + -
671A ILE 3.9 0.4 + - - -
672A LEU* 1.3 72.5 - - - +
674A PHE* 1.3 59.9 + - - +
675A HIS* 4.0 14.6 - - + +
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Residues in contact with PHE 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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606A GLY* 4.7 0.9 - - - -
607A VAL 2.9 16.1 + - - +
608A VAL* 3.3 7.1 - - + -
609A MET 2.7 32.9 + - - +
654A THR 3.8 3.1 - - - -
655A VAL* 3.9 30.5 - - + -
672A LEU* 3.5 35.7 - - + -
673A HIS* 1.3 71.4 - - - +
675A HIS* 1.3 55.0 + - - +
694A PHE* 3.7 23.1 - + + -
697A LYS* 4.2 9.9 - - + -
698A VAL* 3.6 38.8 - - + -
701A SER* 3.4 32.5 - - - -
703A SER* 3.9 11.2 - - - -
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Residues in contact with HIS 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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609A MET* 3.4 35.8 - - + +
611A ASN 2.8 24.7 + - - -
612A ARG* 4.4 9.0 - - + +
613A VAL* 5.5 3.6 - - + -
625A TRP* 4.3 9.5 - + - -
653A TYR* 3.1 5.1 - - - -
654A THR* 2.8 44.5 + - - +
656A ARG* 3.6 29.4 + - - +
673A HIS* 4.0 7.0 - - + -
674A PHE* 1.3 72.3 - - - +
676A TYR* 1.3 72.9 + - - +
677A THR* 3.3 19.9 + - + +
694A PHE* 4.1 1.4 - - - -
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Residues in contact with TYR 676 (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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609A MET 2.8 15.7 + - - +
610A LEU* 3.9 17.3 - - + +
611A ASN 3.8 7.3 - - - +
652A TYR* 3.6 17.9 - - + +
653A TYR* 3.8 3.6 - + + -
675A HIS* 1.3 79.8 - - - +
677A THR* 1.3 60.6 + - - +
678A THR* 3.5 35.8 + - - -
679A TRP* 3.5 29.3 + + + -
685A PRO* 3.6 14.1 - - + +
686A GLU* 3.3 15.2 + - - +
690A SER* 2.7 40.4 + - - -
691A PHE* 4.3 7.6 - + + -
694A PHE* 3.8 36.3 - + + -
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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