Contacts of the strand formed by residues 699 - 706 (chain A) in PDB entry 1QAS
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 LEU 699 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A VAL* 4.5 5.8 - - + -
568A TRP* 4.5 13.5 - - + -
588A VAL* 3.9 21.1 - - + +
592A CYS* 3.8 31.6 - - + +
659A GLU 3.7 0.3 - - - +
660A ILE* 3.5 4.5 - - - +
661A HIS* 2.7 42.9 + - + +
697A LEU 4.1 8.1 - - - +
698A ALA* 1.3 82.8 - - - +
700A VAL* 1.3 64.4 + - - +
701A ARG 4.0 0.4 + - - -
720A THR* 3.7 26.0 - - + -
721A ILE 3.4 8.1 - - - +
722A PRO* 3.9 16.6 - - + -
723A TRP 4.0 1.6 - - - +
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Residues in contact with VAL 700 (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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631A LEU* 3.9 18.4 - - + -
633A VAL* 5.0 1.3 - - + -
658A VAL* 4.2 14.4 - - + -
659A GLU 3.5 7.6 - - - +
660A ILE* 3.5 25.8 - - + -
699A LEU* 1.3 74.6 - - - +
701A ARG* 1.3 61.3 + - - +
702A PHE* 3.9 29.5 + - + -
719A SER 4.1 0.5 - - - +
720A THR* 3.5 1.0 - - - -
721A ILE* 2.7 44.9 + - - +
723A TRP* 4.2 13.7 - - + -
726A LEU* 4.0 20.4 - - + -
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Residues in contact with ARG 701 (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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584A PRO* 3.9 25.4 - - - +
587A ASP* 2.6 29.5 + - - +
588A VAL* 4.1 9.4 - - - -
657A ILE 3.6 0.7 - - - +
658A VAL* 3.3 5.2 - - - +
659A GLU* 2.6 87.4 + - + +
661A HIS* 3.8 14.4 - - + -
699A LEU 4.0 0.2 + - - -
700A VAL* 1.3 73.8 - - - +
702A PHE* 1.3 67.2 + - - +
703A MET* 3.5 32.7 - - - +
715A PHE* 4.2 5.1 - - - -
718A GLN* 2.8 20.5 - - - +
719A SER 3.4 5.6 - - - +
720A THR* 3.1 22.0 - - + +
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Residues in contact with PHE 702 (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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633A VAL* 3.7 31.2 - - + -
635A ILE* 4.0 18.2 - - + -
656A VAL* 4.9 0.7 - - + -
657A ILE 3.6 3.1 - - - -
658A VAL* 4.1 9.6 - - + -
700A VAL* 3.9 27.6 - - + -
701A ARG* 1.3 74.9 - - - +
703A MET* 1.3 60.3 + - - +
704A VAL* 5.3 0.9 - - - -
718A GLN* 3.3 6.4 - - - +
719A SER 2.8 38.6 + - - +
721A ILE* 3.8 25.4 - - + -
726A LEU* 4.4 13.0 - - + -
733A VAL* 4.1 41.3 - - + -
735A LEU* 4.8 1.0 - - + +
748A LEU* 4.3 13.2 - - + -
750A VAL* 4.4 2.0 - - + -
752A ILE* 4.7 7.0 - - + -
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Residues in contact with MET 703 (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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584A PRO* 6.3 1.3 - - + -
655A LYS 3.6 0.7 - - - +
656A VAL* 3.1 5.8 - - - +
657A ILE* 2.6 66.0 + - + +
659A GLU* 5.0 3.1 - - - +
701A ARG* 3.5 41.7 - - + +
702A PHE* 1.3 73.1 - - - +
704A VAL* 1.3 66.6 + - - +
705A GLU* 3.7 36.3 - - + +
715A PHE* 4.2 21.1 - - - -
717A GLY 4.0 0.9 - - - -
718A GLN* 4.0 5.2 - - + -
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Residues in contact with VAL 704 (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* 4.2 19.7 - - + -
654A PRO* 4.2 5.8 - - + -
655A LYS 3.4 9.6 - - - +
656A VAL* 4.2 9.6 - - + -
703A MET* 1.3 79.5 - - - +
705A GLU* 1.3 63.2 - - - +
715A PHE* 3.9 2.4 - - - -
716A ILE* 2.8 45.7 + - + +
717A GLY 2.9 14.7 + - - +
735A LEU* 3.7 30.3 - - + -
748A LEU* 3.7 26.5 - - + -
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Residues in contact with GLU 705 (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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654A PRO* 3.2 7.8 - - - +
655A LYS* 2.9 43.8 + - + +
657A ILE* 3.6 24.4 - - + +
703A MET* 3.7 21.8 - - + +
704A VAL* 1.3 75.4 - - - +
706A ASP* 1.3 61.8 + - - +
707A TYR 3.8 0.6 + - - -
712A LYS* 3.5 22.2 + - - -
713A ASN* 2.8 37.5 + - + +
714A ASP 3.4 9.4 - - - +
715A PHE* 4.9 2.2 - - + -
716A ILE* 3.4 6.9 - - - +
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Residues in contact with ASP 706 (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 ASN* 5.4 0.2 - - - +
651A ILE* 3.2 34.9 - - + +
652A VAL* 3.1 33.0 + - - +
653A ASP 3.4 3.6 + - - -
705A GLU* 1.3 71.7 - - - +
707A TYR* 1.3 70.6 + - - +
708A ASP* 6.2 0.2 - - - -
713A ASN* 3.0 7.4 - - - -
714A ASP* 2.6 60.3 + - + +
716A ILE* 3.9 11.9 - - + -
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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