Contacts of the helix formed by residues 561 - 575 (chain A) in PDB entry 1QU2
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 GLY 561 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A TRP* 3.7 28.0 - - - -
557A ASP 3.2 6.6 + - - -
558A GLN* 3.0 15.3 + - - -
560A ARG* 1.3 78.5 - - - +
562A TRP* 1.3 65.3 + - - -
563A PHE 3.2 2.0 - - - -
564A ASN* 3.0 6.1 + - - +
565A SER* 3.0 23.0 + - - -
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Residues in contact with TRP 562 (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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53A HIS* 3.5 23.8 - + - -
54A ASP 3.7 2.5 - - - -
55A GLY* 3.4 33.0 - - - -
56A PRO* 3.8 9.3 - - + +
528A TRP* 3.6 5.1 - - + -
531A SER* 2.9 46.1 + - - -
532A GLY 4.0 0.9 - - - -
534A SER* 3.1 18.7 + - - -
552A TYR* 3.1 39.5 - + + -
554A GLU* 3.7 25.4 - - + -
558A GLN* 2.8 21.7 + - + +
561A GLY* 1.3 71.2 - - - -
563A PHE* 1.3 64.6 + + - +
565A SER* 4.0 4.3 - - - -
566A SER* 2.6 52.5 + - - -
1993A MRC 3.7 13.9 - - + -
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Residues in contact with PHE 563 (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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441A ILE* 4.2 7.6 - - + -
552A TYR* 4.1 12.3 - + + -
554A GLU* 3.6 48.7 - - + -
555A GLY 4.3 1.6 - - - -
558A GLN* 2.9 31.7 + - + +
559A TYR* 3.8 17.3 - + - -
562A TRP* 1.3 83.0 - + - +
564A ASN* 1.3 55.8 + - - +
566A SER* 4.0 1.4 - - - -
567A ILE* 3.2 21.5 + - - +
579A TYR* 3.2 26.7 + - - +
582A LEU* 3.4 44.9 - - + -
583A LEU 4.0 4.5 - - - -
584A SER* 4.0 17.7 - - - -
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Residues in contact with ASN 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE* 4.7 3.8 - - + -
444A MET* 4.3 14.4 - - + +
445A VAL* 3.9 19.9 - - - +
448A ARG* 2.6 39.1 + - - +
558A GLN 3.7 0.4 + - - -
559A TYR 3.3 21.3 + - - +
560A ARG* 3.5 16.4 + - - +
561A GLY 3.0 7.5 + - - +
563A PHE* 1.3 76.7 - - - +
565A SER* 1.3 60.4 + - - +
566A SER 3.1 1.5 + - - -
567A ILE* 3.2 7.0 - - - +
568A THR* 2.9 38.1 + - - -
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Residues in contact with SER 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 5.1 2.0 - - - +
451A TRP* 3.9 22.7 - - - -
528A TRP* 3.0 37.7 + - - +
531A SER* 4.3 0.9 + - - -
532A GLY* 3.1 11.6 + - - +
561A GLY 3.0 15.1 + - - -
562A TRP* 3.8 9.0 + - - -
564A ASN* 1.3 77.6 - - - +
566A SER* 1.3 62.9 + - - +
568A THR* 4.0 4.8 - - - -
569A THR* 3.2 26.2 + - - +
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Residues in contact with SER 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLY* 3.4 15.1 + - - -
534A SER* 4.7 1.0 + - - -
535A HIS* 3.6 3.1 - - - -
552A TYR* 3.9 22.6 + - - -
562A TRP* 2.6 49.3 + - - -
563A PHE 4.0 2.0 - - - -
565A SER* 1.3 77.2 + - - +
567A ILE* 1.3 60.2 + - - +
569A THR* 3.3 2.9 - - - +
570A SER* 3.0 30.5 + - - -
578A PRO* 3.7 6.2 - - - +
579A TYR* 4.8 0.2 - - - -
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Residues in contact with ILE 567 (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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423A ILE* 3.8 18.2 - - + -
426A ALA* 4.4 6.3 - - + -
427A ILE* 3.8 28.0 - - + +
430A THR* 4.9 0.4 - - - +
441A ILE* 4.6 6.7 - - + -
445A VAL* 5.1 1.1 - - + -
563A PHE 3.2 14.7 + - - +
564A ASN* 3.2 17.0 - - - +
566A SER* 1.3 77.0 - - - +
568A THR* 1.3 67.8 + - - +
571A VAL* 2.8 50.7 + - + +
577A SER* 3.8 23.6 - - - +
578A PRO* 3.7 14.8 - - + +
579A TYR* 3.8 15.9 - - + +
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Residues in contact with THR 568 (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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170A MET* 5.3 6.7 - - + -
416A ILE* 3.5 30.1 - - + +
419A VAL* 4.9 4.8 - - + +
423A ILE* 3.5 27.1 - - + +
445A VAL* 5.2 0.3 - - - +
448A ARG* 3.9 6.7 + - - -
451A TRP* 4.1 15.5 - - + -
564A ASN* 2.9 31.1 + - - -
565A SER* 4.0 6.5 - - - -
567A ILE* 1.3 79.4 - - - +
569A THR* 1.3 62.1 + - - +
571A VAL* 4.2 1.2 - - - +
572A ALA* 3.2 23.2 + - - +
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Residues in contact with THR 569 (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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166A ILE* 3.3 25.3 - - + +
170A MET* 4.1 9.4 - - - -
451A TRP* 5.1 6.2 - - - -
529A PHE* 4.3 9.0 - - - -
532A GLY 2.8 23.6 - - - +
533A SER* 4.3 2.6 - - - -
535A HIS* 2.7 36.3 - - + +
565A SER 3.2 10.6 + - - +
566A SER 3.3 4.9 - - - +
568A THR* 1.3 80.9 - - - +
570A SER* 1.3 61.3 + - - +
572A ALA* 3.5 5.0 + - - +
573A THR* 3.0 30.3 + - - +
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Residues in contact with SER 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS* 3.5 21.1 - - - -
547A PHE* 3.2 22.9 - - - -
566A SER 3.0 16.7 + - - -
567A ILE 3.9 0.2 - - - -
569A THR* 1.3 79.6 - - - +
571A VAL* 1.3 56.2 + - - +
573A THR* 4.0 0.9 - - - -
574A ARG* 2.6 40.1 + - - +
575A GLY 3.2 0.2 + - - -
576A VAL 2.7 22.7 + - - -
578A PRO* 3.5 14.3 - - - +
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Residues in contact with VAL 571 (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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419A VAL* 4.8 2.2 - - + +
422A ASP* 3.7 39.5 - - + +
423A ILE* 4.0 15.9 - - + +
426A ALA* 3.9 20.2 - - + -
567A ILE* 2.8 41.7 + - + +
570A SER* 1.3 71.9 - - - +
572A ALA* 1.3 63.0 + - - +
575A GLY* 2.8 35.3 + - - +
576A VAL 4.0 10.3 - - - +
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Residues in contact with ALA 572 (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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170A MET* 4.0 20.6 - - + -
173A LYS* 3.1 29.5 - - - +
175A LEU* 3.8 21.7 - - + +
419A VAL* 4.3 18.1 - - + +
568A THR 3.2 17.8 + - - +
569A THR 3.7 5.4 - - - +
570A SER 3.3 0.2 - - - -
571A VAL* 1.3 81.3 - - - +
573A THR* 1.3 57.7 + - - +
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Residues in contact with THR 573 (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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166A ILE* 3.9 13.9 - - + +
169A GLU* 3.3 34.5 - - + +
170A MET* 3.7 23.8 - - + +
173A LYS* 4.3 11.5 + - - +
535A HIS* 4.6 3.8 - - - -
536A ARG* 3.9 10.9 + - - -
569A THR 3.0 18.5 + - - +
570A SER* 3.7 3.6 + - - -
571A VAL 3.2 0.2 - - - -
572A ALA* 1.3 83.0 - - - +
574A ARG* 1.3 76.1 + - - +
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Residues in contact with ARG 574 (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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169A GLU* 3.9 8.7 + - - -
535A HIS* 5.3 2.2 - - + -
536A ARG* 3.2 36.3 - - - +
540A GLU* 2.7 39.1 + - - +
547A PHE* 3.9 33.4 - - + -
570A SER* 2.6 22.1 + - - +
573A THR* 1.3 94.6 + - - +
575A GLY* 1.3 58.8 + - - +
576A VAL* 3.1 12.9 + - + +
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Residues in contact with GLY 575 (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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422A ASP 5.6 0.3 - - - +
426A ALA* 5.1 4.3 - - - +
570A SER 3.2 1.2 + - - -
571A VAL* 2.8 30.7 + - - +
573A THR 3.8 0.4 - - - -
574A ARG* 1.3 77.4 - - - +
576A VAL* 1.3 64.7 + - - +
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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
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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