Contacts of the strand formed by residues 646 - 654 (chain A) in PDB entry 1QHP
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 THR 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A ASN* 5.0 4.3 + - - +
606A ILE* 5.9 1.0 - - - +
645A LYS* 1.3 74.7 - - - +
647A ILE* 1.3 64.2 + - - +
648A GLN* 5.9 1.1 - - + -
669A VAL* 3.7 27.4 - - + -
670A ALA 3.3 7.4 - - - +
671A THR* 2.8 22.0 + - - +
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Residues in contact with ILE 647 (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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586A PHE* 3.9 28.5 - - + -
605A ASN* 3.8 8.5 - - - +
606A ILE* 3.8 30.7 - - + -
609A LEU* 4.1 11.9 - - + -
641A VAL* 4.9 2.7 - - + -
642A PRO* 4.8 0.9 - - + -
645A LYS* 4.1 14.8 - - + +
646A THR* 1.3 78.8 - - - +
648A GLN* 1.3 67.4 + - - +
649A PHE* 4.0 17.8 - - + -
668A HIS 3.8 0.2 - - - +
669A VAL* 3.4 6.4 - - - +
670A ALA 2.8 41.2 + - - +
672A THR* 3.9 21.3 - - + -
680A ILE* 4.4 2.7 - - + -
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Residues in contact with GLN 648 (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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604A GLY* 3.2 2.8 - - - -
605A ASN* 2.9 51.1 + - + +
609A LEU* 4.6 0.7 - - - +
612A TRP* 3.9 4.9 - - + -
646A THR* 6.0 1.1 - - + +
647A ILE* 1.3 79.6 - - - +
649A PHE* 1.3 63.5 + - - +
667A ASN* 2.9 33.2 + - - +
668A HIS 3.2 6.3 - - - +
669A VAL* 4.2 25.1 - - + +
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Residues in contact with PHE 649 (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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586A PHE* 4.2 7.4 - + - -
602A LEU* 3.7 23.6 - - + -
603A THR 3.3 14.1 - - - +
604A GLY* 4.1 2.5 - - - -
609A LEU* 4.1 6.5 - - + -
612A TRP* 3.7 6.4 - - - -
647A ILE* 4.0 19.7 - - + -
648A GLN* 1.3 79.2 - - - +
650A LYS* 1.3 65.0 + - - +
651A PHE* 3.8 24.9 - + - -
667A ASN* 3.9 0.4 - - - +
668A HIS* 2.9 64.9 + + + +
670A ALA* 3.9 24.7 - - + -
680A ILE* 3.7 24.9 - - + -
682A VAL* 4.0 8.7 - - + -
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Residues in contact with LYS 650 (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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602A LEU* 3.7 3.9 - - - +
603A THR* 2.9 33.7 + - - +
612A TRP* 3.8 2.3 - - + -
649A PHE* 1.3 80.5 - - - +
651A PHE* 1.3 71.6 + - - +
662A TRP* 4.1 16.8 - - + -
663A GLU* 2.9 39.8 + - + +
664A ASN 3.5 7.6 + - - -
665A GLY 2.7 29.7 + - - -
666A SER 3.8 9.9 - - - +
667A ASN* 3.7 22.4 - - - +
668A HIS* 4.4 2.9 - - + +
685A GLN* 4.7 0.4 - - - +
1D GLC 2.8 37.2 + - - +
2D GLC 4.2 0.9 - - - +
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Residues in contact with PHE 651 (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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586A PHE* 4.4 15.9 - + + -
587A THR 4.6 4.3 - - - -
588A VAL* 3.7 23.8 - - + -
600A ILE* 4.1 3.8 - - + -
601A TYR 3.2 15.7 - - - +
602A LEU* 3.7 29.4 - - + -
627A LEU* 3.8 29.6 - - + -
649A PHE* 3.8 18.2 - + - -
650A LYS* 1.3 79.4 - - - +
652A PHE* 1.3 63.2 + - - +
662A TRP* 4.0 1.0 - - - -
663A GLU* 3.0 43.5 + - - +
682A VAL* 3.6 26.0 - - + -
684A TRP* 3.6 20.6 - - + -
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Residues in contact with PHE 652 (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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600A ILE* 3.3 3.6 - - - +
601A TYR* 2.9 68.9 + + + -
603A THR* 3.9 23.1 - - + -
613A SER 3.9 4.5 - - - -
614A THR* 3.6 29.2 - - + -
616A THR* 4.4 0.7 - - + -
623A ALA* 3.6 26.0 - - + -
651A PHE* 1.3 76.0 - - - +
653A ILE* 1.3 72.1 + - - +
654A LYS* 4.2 3.1 - - + -
660A ILE* 3.8 32.5 - - + -
661A GLN 3.3 13.9 - - - +
662A TRP* 3.9 15.0 - + + -
684A TRP* 3.9 4.0 - - - -
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Residues in contact with ILE 653 (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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592A PRO* 4.1 31.9 - - + +
594A THR* 4.3 11.2 - - + -
598A ASP* 4.2 9.2 - - + -
599A LYS 3.6 7.2 - - - +
600A ILE* 3.8 19.5 - - + -
652A PHE* 1.3 75.8 - - - +
654A LYS* 1.3 66.6 - - - +
655A ARG* 3.6 52.4 + - - +
659A THR 3.6 1.4 - - - +
660A ILE* 3.4 4.0 - - - -
661A GLN* 2.8 44.0 + - + +
684A TRP* 3.8 12.1 - - + -
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Residues in contact with LYS 654 (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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597A GLY 4.2 1.0 - - - +
598A ASP* 3.5 0.5 - - - -
599A LYS 2.8 35.9 + - - +
601A TYR* 4.0 18.8 - - + +
614A THR 5.0 2.6 + - - +
616A THR* 2.7 39.6 + - + +
652A PHE* 3.9 2.6 + - + -
653A ILE* 1.3 73.0 - - - +
655A ARG* 1.3 73.5 + - - +
658A GLY* 3.9 22.4 - - - +
659A THR 3.4 4.9 - - - +
660A ILE* 3.8 21.5 - - + -
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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