Contacts of the strand formed by residues 593 - 608 (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 VAL 593 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ALA 3.6 0.2 - - - -
589A LEU* 2.6 59.7 + - + -
590A SER* 3.1 17.6 + - - +
591A ALA 3.7 0.2 - - - -
592A SER* 1.3 76.8 - - - +
594A ASN* 1.3 62.7 + - - +
595A VAL* 4.2 11.9 - - + -
629A ALA* 5.9 1.1 - - + -
630A ASP 3.3 6.7 - - - +
631A TYR* 3.0 37.9 - - + -
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Residues in contact with ASN 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER* 4.5 6.7 + - - -
22A TRP* 3.7 17.9 - - + +
23A GLY* 3.8 21.5 - - - -
24A PRO* 4.4 1.2 - - - +
587A ALA 3.7 4.9 - - - +
588A ALA* 3.2 29.1 - - - +
590A SER 4.9 1.4 - - - +
591A ALA 5.8 2.2 + - - -
592A SER 5.4 1.2 - - - -
593A VAL* 1.3 76.5 - - - +
595A VAL* 1.3 69.3 + - - +
628A TRP* 4.3 2.6 - - + -
629A ALA* 3.3 1.0 - - - -
630A ASP* 2.6 62.5 + - - +
632A THR* 5.3 1.4 + - - -
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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
----------------------------------------------------------
585A ALA 5.6 1.8 - - - +
586A LYS* 3.2 1.6 - - - -
587A ALA* 2.7 49.4 + - + +
589A LEU* 4.5 19.3 - - + -
593A VAL* 4.2 15.0 - - + -
594A ASN* 1.3 85.1 - - - +
596A VAL* 1.3 66.7 + - - +
627A LEU* 5.4 10.5 - - + -
628A TRP* 3.2 10.1 - - - +
629A ALA* 3.7 18.2 - - + -
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Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 5.0 7.0 - - - +
61A HIS* 5.3 4.7 - - + -
72A TYR* 4.0 22.8 - - + +
584A GLU* 5.4 0.7 - - - +
585A ALA 3.1 4.7 - - - -
586A LYS* 2.8 46.4 - - + -
595A VAL* 1.3 77.4 - - - +
597A GLY* 1.3 54.4 + - - +
627A LEU* 3.7 4.5 - - - +
628A TRP* 2.7 59.9 + - + +
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Residues in contact with GLY 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.9 9.9 + - - -
583A ILE* 5.9 0.4 - - - -
584A GLU* 3.5 3.5 - - - +
585A ALA* 2.6 38.5 + - - +
596A VAL* 1.3 77.3 - - - +
598A SER* 1.3 64.4 + - - -
626A SER* 3.3 12.8 - - - -
627A LEU* 3.9 12.5 - - - +
1101A DDQ 5.9 0.2 - - - -
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Residues in contact with SER 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR 3.5 11.4 + - - -
73A THR 3.5 18.2 + - - -
74A PRO* 3.5 18.2 - - - +
583A ILE* 3.1 19.3 - - - -
597A GLY* 1.3 78.0 - - - -
599A TYR* 1.3 64.5 + - - +
600A THR* 4.8 1.0 + - - -
625A ALA* 3.3 6.8 - - - +
626A SER* 2.6 43.2 + - - +
1101A DDQ 4.3 7.1 - - - +
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Residues in contact with TYR 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 4.1 0.3 - - - +
581A VAL* 4.8 6.5 - - + -
582A GLU* 3.4 3.1 - - - -
583A ILE* 2.8 59.7 + - + +
598A SER* 1.3 78.3 - - - +
600A THR* 1.3 84.4 + - - +
601A TYR* 3.7 16.2 - - + +
623A HIS* 2.5 38.6 + - + -
624A MET 3.6 10.8 - - - -
625A ALA* 3.9 2.2 - - + -
1101A DDQ 3.7 47.2 - - + +
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Residues in contact with THR 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR 4.8 0.2 + - - -
74A PRO* 3.5 7.8 - - - +
75A GLY* 2.9 40.5 + - - +
552A TYR* 5.7 1.6 - - - +
581A VAL 3.3 2.7 - - - +
582A GLU* 3.9 13.0 - - + +
598A SER* 4.8 1.2 + - - -
599A TYR* 1.3 87.7 - - - +
601A TYR* 1.3 64.4 + - - +
602A THR* 3.5 20.6 - - - +
622A LYS 3.6 0.3 - - - +
623A HIS* 3.6 4.2 - - - -
624A MET* 2.8 52.9 + - + +
625A ALA* 5.9 0.2 - - - -
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Residues in contact with TYR 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A TYR* 4.6 0.9 + - - -
579A ARG* 4.9 8.0 + - + -
580A GLY* 3.0 9.7 - - - -
581A VAL* 2.7 61.7 + - + +
599A TYR* 3.7 15.7 - - + +
600A THR* 1.3 77.5 - - - +
602A THR* 1.3 62.2 + - - +
603A ASP* 4.1 21.3 - - + +
622A LYS* 2.9 46.7 + - + -
623A HIS* 3.3 32.3 - + - -
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Residues in contact with THR 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY* 5.6 0.2 - - - -
93A ARG* 4.3 4.1 - - - +
94A GLY 4.3 19.9 + - - +
552A TYR* 3.5 20.9 + - - +
578A ALA* 4.7 2.5 - - + -
579A ARG 3.9 2.2 - - - +
600A THR* 3.5 18.7 - - - +
601A TYR* 1.3 77.2 - - - +
603A ASP* 1.3 64.8 + - - +
604A ALA* 3.6 7.0 + - + -
620A VAL* 4.5 13.3 - - + +
621A PRO 3.8 14.4 + - - +
622A LYS* 2.8 33.4 + - - +
624A MET* 4.5 7.3 - - - +
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Residues in contact with ASP 603 (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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577A ARG* 3.7 5.9 + - - +
578A ALA* 3.3 1.7 - - - -
579A ARG* 2.3 89.1 + - - +
601A TYR* 4.1 22.8 - - + +
602A THR* 1.3 71.2 - - - +
604A ALA* 1.3 64.4 + - - +
605A GLU* 4.7 8.8 - - - +
616A THR* 5.4 3.3 - - - +
622A LYS* 4.5 14.6 - - - +
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Residues in contact with ALA 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY* 4.9 6.3 - - - +
95A PHE* 6.0 0.4 - - + -
576A ILE* 5.2 2.7 - - + -
577A ARG 3.1 6.3 - - - +
578A ALA* 4.0 12.8 - - + +
602A THR* 3.6 7.6 + - + -
603A ASP* 1.3 73.9 + - - +
605A GLU* 1.3 61.4 + - - +
616A THR* 3.0 36.5 - - - +
617A PRO* 4.1 22.4 - - + -
620A VAL* 4.4 19.7 - - + +
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Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A ILE* 3.4 5.9 - - - +
577A ARG* 2.4 85.5 + - + +
579A ARG* 4.6 4.0 + - - -
603A ASP* 4.7 8.9 - - - +
604A ALA* 1.3 71.7 - - - +
606A TYR* 1.3 75.7 + - - +
607A THR* 2.9 11.6 + - - +
614A GLY* 3.5 25.7 - - - +
615A ASN 3.8 2.0 - - - -
616A THR* 5.5 1.3 - - + +
617A PRO* 4.4 1.0 - - - +
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Residues in contact with TYR 606 (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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559A ASN* 4.2 6.5 - - - -
575A GLU 5.0 1.1 - - - -
576A ILE* 3.5 32.8 - - + +
605A GLU* 1.3 76.1 - - - +
607A THR* 1.3 59.8 + - - +
608A THR 3.8 1.6 - - - -
609A ASP* 4.1 25.4 - - + -
612A TYR* 3.4 48.1 - + + +
613A LYS* 4.0 1.5 - - - +
614A GLY 2.8 27.5 + - - -
615A ASN* 2.8 31.3 + - + +
616A THR 4.4 0.2 - - - -
617A PRO* 4.1 30.2 - - + +
657A PRO* 4.1 22.7 - - + +
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Residues in contact with THR 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A GLU* 2.8 42.3 + - + +
576A ILE* 4.6 1.1 - - - -
577A ARG* 4.2 18.4 + - - +
605A GLU* 2.9 14.3 + - - +
606A TYR* 1.3 73.2 - - - +
608A THR* 1.3 74.5 + - - +
613A LYS* 2.9 27.0 + - - -
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Residues in contact with THR 608 (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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559A ASN* 5.9 0.2 + - - -
561A MET* 4.7 9.2 - - + -
573A GLY 3.9 15.2 + - - +
574A GLY* 3.4 6.6 - - - -
575A GLU* 2.9 40.4 + - - +
606A TYR* 5.2 0.7 - - - -
607A THR* 1.3 91.7 + - - +
609A ASP* 1.3 68.8 + - - +
613A LYS* 4.7 4.7 - - + +
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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
------------------------------------------------------------
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