Contacts of the strand formed by residues 590 - 601 (chain A) in PDB entry 1QWN
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 ALA 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A VAL* 4.0 16.2 - - + +
588A VAL 4.2 2.2 - - - +
589A GLU* 1.3 79.3 - - - +
591A GLN* 1.3 59.6 + - - +
618A ILE* 3.9 20.6 - - + -
619A ILE 3.2 12.1 - - - +
620A PHE* 4.2 0.7 - - + -
643A HIS 2.9 7.3 + - - +
644A THR* 3.3 19.6 - - - +
645A SER* 2.9 26.7 + - - -
752A LEU* 4.0 4.9 - - - -
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Residues in contact with GLN 591 (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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590A ALA* 1.3 75.0 - - - +
592A VAL* 1.3 72.0 + - - +
593A SER* 3.0 21.2 + - - +
617A ARG 3.7 0.7 - - - +
618A ILE* 3.4 2.1 - - - +
619A ILE* 2.8 47.8 + - + +
645A SER* 3.4 16.4 - - - +
646A TYR 5.0 0.2 - - - -
647A ALA* 3.8 12.1 - - - +
748A THR* 5.1 0.6 - - - +
750A GLY* 3.7 7.6 - - - -
751A LYS 3.3 3.8 + - - -
752A LEU* 2.8 44.6 + - + -
753A GLU* 3.0 31.6 + - - +
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Residues in contact with VAL 592 (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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573A VAL* 5.6 1.8 - - + -
576A PRO* 3.8 18.8 - - + +
578A VAL* 5.4 1.3 - - + +
591A GLN* 1.3 76.4 - - - +
593A SER* 1.3 66.8 + - - +
616A TYR* 4.0 22.7 - - + -
617A ARG 3.1 10.5 - - - +
618A ILE* 4.0 19.3 - - + -
644A THR* 3.6 22.2 - - + -
645A SER 2.8 7.7 + - - -
646A TYR* 3.4 27.1 - - + -
647A ALA 3.1 25.1 + - - -
664A TYR* 3.3 10.6 + - + -
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Residues in contact with SER 593 (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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591A GLN* 3.0 28.3 + - - -
592A VAL* 1.3 72.7 - - - +
594A PRO* 1.3 75.0 - - - +
596A TRP* 6.1 0.4 - - - -
616A TYR* 3.8 4.9 - - - +
617A ARG* 2.8 51.2 + - - -
619A ILE* 3.7 7.2 - - - +
647A ALA* 3.6 7.3 - - - +
664A TYR* 3.6 6.7 - - - -
748A THR* 4.2 8.5 - - - +
753A GLU* 5.0 0.3 + - - -
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Residues in contact with PRO 594 (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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593A SER* 1.3 96.0 - - - +
595A VAL* 1.3 63.3 + - - +
596A TRP* 3.6 30.7 + - + +
612A SER 5.5 0.7 - - - +
616A TYR* 4.6 9.4 - - + -
617A ARG* 3.8 14.6 + - - -
649A ASN* 3.4 31.0 - - - +
661A LEU* 3.7 32.1 - - + -
664A TYR* 3.5 19.7 - - + +
748A THR* 4.9 0.9 - - + -
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Residues in contact with VAL 595 (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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572A TYR* 3.8 41.3 - - + +
594A PRO* 1.3 71.5 - - - +
596A TRP* 1.3 66.6 + - - +
597A SER* 5.9 2.2 - - - -
610A GLN 3.7 1.4 - - - +
611A GLY* 3.4 3.7 - - - -
612A SER* 3.0 32.5 + - - +
615A LYS* 3.7 40.7 + - + +
616A TYR* 3.7 20.6 - - - +
617A ARG* 3.8 6.5 - - + +
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Residues in contact with TRP 596 (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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534A SER* 4.0 13.5 + - - -
593A SER* 6.1 0.2 - - - -
594A PRO* 3.6 32.3 + - + +
595A VAL* 1.3 76.3 - - - +
597A SER* 1.3 60.8 + - - +
598A TRP* 4.8 8.1 - - - +
609A PRO* 4.0 20.2 - - + -
610A GLN 3.4 6.7 - - - -
611A GLY* 3.6 33.4 - - - -
617A ARG* 5.9 0.4 - - - +
649A ASN* 3.1 41.6 + - + -
659A LEU* 4.1 24.2 - - + -
661A LEU* 4.2 7.2 - - + -
668A VAL* 4.0 21.1 - - + -
746A LEU* 3.6 30.5 - - + -
748A THR* 3.9 8.2 + - + -
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Residues in contact with SER 597 (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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534A SER* 5.2 4.9 - - - -
535A GLY* 6.2 2.9 - - - -
595A VAL* 4.2 3.1 + - - -
596A TRP* 1.3 76.2 - - - +
598A TRP* 1.3 62.7 + - - +
599A HIS* 3.0 28.8 + - - -
609A PRO* 3.3 0.4 - - - +
610A GLN* 2.7 42.9 + - - +
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Residues in contact with TRP 598 (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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535A GLY* 6.1 2.4 - - - -
596A TRP* 4.8 7.3 - - - +
597A SER* 1.3 80.7 - - - +
599A HIS* 1.3 69.0 + - - +
607A ILE* 3.6 26.2 - - + -
608A HIS* 3.6 20.2 - - - -
609A PRO* 3.6 28.3 - - + +
744A VAL* 3.4 22.7 - - + -
746A LEU* 4.0 17.4 - - + +
757A SER* 3.7 34.8 - - - -
758A VAL 4.2 0.2 - - - -
759A GLY* 3.5 20.2 - - - -
764A VAL* 3.7 37.4 - - + +
766A GLN* 5.7 1.7 - - - +
779A LEU* 5.7 6.1 - - + +
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Residues in contact with HIS 599 (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 SER* 3.0 37.7 + - - -
598A TRP* 1.3 81.1 + - - +
600A HIS* 1.3 63.7 + - - +
601A ASP* 3.3 6.9 + - + +
606A THR 3.6 0.2 - - - +
607A ILE* 3.3 5.7 - - - -
608A HIS* 2.9 39.8 + - + +
610A GLN* 3.2 31.5 - - + +
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Residues in contact with HIS 600 (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 HIS* 1.3 72.2 - - - +
601A ASP* 1.3 73.4 + - - +
602A THR* 3.2 32.7 + - + +
605A LYS* 4.5 19.1 + - + +
606A THR 3.7 8.2 + - - -
607A ILE* 3.9 22.0 - - + +
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Residues in contact with ASP 601 (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 HIS* 3.3 4.1 + - + -
600A HIS* 1.3 72.9 - - - +
602A THR* 1.3 52.9 + - - +
603A LEU* 3.0 24.1 + - - +
604A THR* 3.0 32.1 + - - +
605A LYS* 2.8 35.9 + - - -
606A THR 2.8 16.8 + - - +
608A HIS* 2.8 31.4 + - - +
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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