Contacts of the helix formed by residues 583 - 600 (chain A) in PDB entry 1Q8Z
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 CYS 583 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A HIS* 3.3 58.8 + - + +
289A GLY 5.6 0.7 - - - -
290A ILE 4.8 1.3 - - - -
291A ILE* 3.8 26.9 - - - +
557A TYR* 4.7 5.8 - - - -
582A GLY* 1.3 70.5 - - - +
584A GLY* 1.3 56.0 + - - +
585A ALA 2.8 11.6 + - - -
586A ASP* 2.9 14.6 + - - +
587A ILE 4.1 0.2 + - - -
729A ILE* 4.8 1.6 - - - -
730A PRO 4.3 8.5 - - - -
731A GLY 3.1 21.6 + - - -
732A TRP* 3.0 17.3 + - + -
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Residues in contact with GLY 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A GLY 5.5 0.2 - - - -
583A CYS* 1.3 77.3 - - - +
585A ALA* 1.3 62.6 + - - +
586A ASP 3.2 0.7 - - - -
587A ILE* 2.9 19.7 + - - +
588A TRP 3.3 0.7 + - - -
691A PRO* 5.4 2.7 - - - -
694A ARG* 3.0 21.5 + - - -
732A TRP* 3.1 45.2 + - - -
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Residues in contact with ALA 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 5.3 3.6 - - + -
293A THR* 5.8 1.3 - - - -
565A ILE* 4.6 13.5 - - + -
566A GLN* 2.9 35.1 + - - +
572A SER* 4.2 8.5 - - - +
574A GLU* 4.2 6.3 + - - +
581A TRP* 4.6 6.5 - - + -
582A GLY 3.1 16.2 + - - +
583A CYS 2.8 4.2 + - - -
584A GLY* 1.3 73.8 - - - +
586A ASP* 1.3 62.6 + - - +
588A TRP* 3.1 12.5 + - - +
589A SER 3.1 5.4 + - - -
694A ARG* 3.7 10.4 - - - +
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Residues in contact with ASP 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 4.3 9.1 - - + +
285A HIS* 3.0 30.8 - - + +
291A ILE* 3.2 7.4 - - - +
292A HIS* 3.1 20.3 + - - +
293A THR* 2.9 29.2 + - - -
295A ILE* 3.5 24.9 - - + +
566A GLN* 5.3 0.2 + - - -
583A CYS 2.9 8.6 + - - +
585A ALA* 1.3 76.2 - - - +
587A ILE* 1.3 52.5 + - - +
589A SER* 3.1 8.3 + - - -
590A THR* 2.7 39.5 + - - -
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Residues in contact with ILE 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 5.3 2.5 - - + -
281A LEU* 4.6 7.9 - - + -
285A HIS* 4.3 11.2 - - - +
583A CYS 4.5 0.9 - - - +
584A GLY* 2.9 10.0 + - - +
586A ASP* 1.3 78.0 - - - +
588A TRP* 1.3 62.0 + - - +
590A THR* 3.5 4.9 + - - -
591A ALA 3.2 16.5 + - - -
686A MET* 3.5 39.1 - - + +
694A ARG* 4.0 4.7 - - + -
695A ALA 3.3 15.9 - - - +
697A ALA* 3.6 36.3 - - + +
700A LEU* 4.2 3.1 - - + -
732A TRP* 3.3 30.7 - - + -
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Residues in contact with TRP 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TYR 3.7 2.5 - - - -
571A ARG 3.0 27.0 + - - -
572A SER* 3.6 10.5 - - - -
573A PRO* 3.7 29.6 - - + -
584A GLY 3.3 2.0 + - - -
585A ALA 3.1 10.1 + - - +
587A ILE* 1.3 77.7 - - - +
589A SER* 1.3 67.1 + - - +
591A ALA* 3.2 5.5 + - - +
592A CYS* 3.1 35.7 + - - -
604A PHE* 3.4 24.9 - + - -
622A ILE* 3.9 15.3 - - + -
626A LEU* 3.7 20.0 - - + -
686A MET 3.8 8.2 + - - -
687A LEU* 3.3 46.2 - - + -
688A GLN 4.3 0.7 - - - -
689A LEU* 3.9 13.2 - - + -
694A ARG* 3.8 25.1 - - - +
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Residues in contact with SER 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A THR 5.6 0.2 - - - -
295A ILE* 3.5 35.0 + - - +
566A GLN* 3.0 20.4 + - - +
570A TYR* 2.8 33.1 + - - +
585A ALA 3.1 1.3 + - - -
586A ASP* 3.1 10.5 + - - -
588A TRP* 1.3 80.2 - - - +
590A THR* 1.3 57.4 + - - +
592A CYS* 3.1 5.7 + - - +
593A LEU* 2.9 27.9 + - - +
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Residues in contact with THR 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.3 26.9 - - + +
278A LEU* 4.1 18.2 - - + -
281A LEU* 3.2 21.0 - - - +
295A ILE* 4.0 7.1 - - - +
586A ASP 2.7 22.7 + - - -
587A ILE* 3.6 8.7 - - - -
589A SER* 1.3 73.3 - - - +
591A ALA* 1.3 56.6 + - - +
593A LEU* 3.1 7.4 + - - +
594A ILE* 2.8 47.3 + - + +
686A MET* 4.3 4.0 - - - -
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Residues in contact with ALA 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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587A ILE 3.2 3.9 + - - +
588A TRP 3.2 8.9 + - - +
590A THR* 1.3 79.1 - - - +
592A CYS* 1.3 63.6 + - - +
594A ILE* 3.5 1.6 + - - +
595A PHE* 3.1 24.3 + - - +
603A LEU* 5.0 1.9 - - - +
683A LEU* 4.2 14.8 - - + +
686A MET* 3.5 36.3 - - + -
687A LEU* 3.6 25.7 - - + +
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Residues in contact with CYS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A GLU 3.8 17.9 - - - +
570A TYR* 3.9 17.7 - - + -
588A TRP* 3.1 44.7 + - - -
589A SER 3.1 8.0 + - - +
591A ALA* 1.3 78.0 - - - +
593A LEU* 1.3 61.7 + - - +
595A PHE* 3.4 2.8 + - - +
596A GLU* 3.1 23.1 + - - +
603A LEU* 4.5 20.1 + - + +
604A PHE* 4.0 18.6 - - - -
687A LEU* 4.7 1.1 - - - -
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Residues in contact with LEU 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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253A LEU* 4.5 9.0 - - + -
257A ILE* 5.5 0.2 - - + -
273A ILE* 5.8 1.1 - - + -
277A LEU* 4.2 20.4 - - + -
295A ILE* 4.2 11.7 - - + -
296A LYS 4.3 2.2 - - - -
297A PRO* 3.2 43.1 - - + -
300A VAL* 4.1 24.9 - - + -
570A TYR* 4.1 10.2 - - + -
589A SER 2.9 13.8 + - - +
590A THR 3.4 7.2 - - - +
592A CYS* 1.3 76.9 - - - +
594A ILE* 1.3 59.1 + - + +
596A GLU* 3.1 9.1 + - + +
597A LEU* 2.8 44.4 + - + +
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Residues in contact with ILE 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 4.4 2.7 - - + -
273A ILE* 6.3 0.2 - - + -
274A SER* 3.3 42.0 - - - +
277A LEU* 5.3 2.5 - - + -
278A LEU* 5.3 1.3 - - + -
590A THR* 2.8 42.3 + - + +
591A ALA 3.9 3.1 - - - +
593A LEU* 1.3 69.7 - - + +
595A PHE* 1.3 67.6 + - - +
597A LEU* 3.0 14.0 + - + +
598A ILE* 2.8 45.7 + - + +
682A PHE* 3.9 21.8 - - + -
683A LEU* 3.6 17.7 - - + -
686A MET* 4.2 7.0 - - + -
705A TRP* 4.7 0.9 - - + -
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Residues in contact with PHE 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ALA 3.1 18.1 + - - +
592A CYS 3.6 4.3 - - - +
594A ILE* 1.3 76.5 - - - +
596A GLU* 1.3 54.8 + - - +
598A ILE* 3.1 10.7 + - + +
599A THR* 2.8 70.1 + - + +
601A ASP 3.5 10.8 - - - -
602A PHE 3.9 4.3 - - - -
603A LEU* 3.5 49.1 - - + -
661A LEU* 3.7 22.9 - - + -
664A VAL* 4.4 9.0 - - + -
665A LEU* 4.2 12.6 - - + -
669A TYR* 3.7 20.4 - + - -
683A LEU* 4.6 11.9 - - + +
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Residues in contact with GLU 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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254A LEU* 5.8 1.0 - - - +
257A ILE* 3.9 27.9 - - + +
262A HIS* 6.1 0.5 - - - -
297A PRO* 4.1 5.3 - - - +
570A TYR* 2.4 41.8 + - - -
592A CYS 3.1 8.4 + - - +
593A LEU* 3.1 10.0 + - + +
595A PHE* 1.3 81.1 - - - +
597A LEU* 1.3 56.0 + - - +
599A THR* 3.9 0.2 - - - -
600A GLY* 2.6 36.3 + - - +
601A ASP 3.2 31.4 - - - +
602A PHE* 3.6 22.3 - - - +
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Residues in contact with LEU 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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253A LEU* 3.9 27.6 - - + -
257A ILE* 4.2 14.8 - - + -
264A GLY* 4.1 0.9 - - - -
265A ILE* 3.1 58.0 + - + +
270A VAL* 3.9 19.0 - - + +
273A ILE* 3.7 36.1 - - + -
274A SER* 5.1 0.4 - - - +
593A LEU* 2.8 27.6 + - + +
594A ILE* 3.0 19.3 + - + +
596A GLU* 1.3 77.5 - - - +
598A ILE* 1.3 58.4 + - - +
600A GLY* 5.1 0.2 - - - -
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Residues in contact with ILE 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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263A ARG 4.9 0.3 - - - +
264A GLY* 3.6 12.6 - - - -
265A ILE 4.2 5.7 + - - +
267A LEU* 4.2 12.9 - - + +
270A VAL* 3.8 21.8 - - + -
594A ILE* 2.8 35.0 + - + +
595A PHE* 3.5 9.9 - - + +
597A LEU* 1.3 77.6 - - - +
599A THR* 1.3 63.3 + - + +
665A LEU* 5.4 2.2 - - + -
671A PHE* 3.6 36.5 - - + -
679A ILE* 4.1 22.4 - - + -
683A LEU* 4.6 2.0 - - + -
705A TRP* 3.8 18.4 - - + -
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Residues in contact with THR 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A HIS 3.5 3.6 - - - +
263A ARG 3.4 20.4 - - - +
264A GLY* 3.9 2.9 - - - -
595A PHE* 2.8 53.8 + - + +
598A ILE* 1.3 86.7 - - + +
600A GLY* 1.3 58.6 + - - +
601A ASP* 3.0 25.0 + - - +
665A LEU* 4.6 3.6 - - + -
669A TYR* 3.6 41.2 - - + -
671A PHE* 5.2 0.7 - - + -
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Residues in contact with GLY 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.7 7.6 - - - +
262A HIS* 3.5 46.1 - - - +
264A GLY* 4.2 5.3 - - - -
265A ILE* 6.6 0.2 - - - -
596A GLU* 2.6 27.8 + - - +
597A LEU 5.1 0.4 - - - -
598A ILE 3.8 0.2 - - - -
599A THR* 1.3 73.6 - - - +
601A ASP* 1.3 64.4 + - - +
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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
------------------------------------------------------------
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