Contacts of the helix formed by residues 583 - 600 (chain B) in PDB entry 1Q99
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B HIS* 3.4 36.9 + - + -
290B ILE 5.0 1.8 - - - -
291B ILE* 3.4 27.6 - - - +
557B TYR* 4.6 6.5 - - - -
582B GLY* 1.3 69.2 - - - -
584B GLY* 1.3 52.8 + - - +
586B ASP* 2.8 36.7 + - - +
587B ILE* 3.9 0.5 + - - +
729B ILE* 4.9 1.8 - - - -
730B PRO 4.0 13.7 - - - -
731B GLY 3.1 20.1 + - - +
732B TRP* 3.3 27.5 + - + -
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Residues in contact with GLY 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLY 2.9 0.6 + - - -
583B CYS* 1.3 78.0 - - - +
585B ALA* 1.3 61.6 + - - +
587B ILE* 2.9 14.9 + - - +
588B TRP 3.2 5.5 + - - -
691B PRO* 5.4 1.3 - - - -
694B ARG* 3.2 23.2 + - - -
732B TRP* 3.0 44.4 + - - -
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Residues in contact with ALA 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 5.0 2.9 - - + -
293B THR* 5.8 1.1 - - - -
565B ILE* 4.6 6.1 - - + -
566B GLN* 2.9 34.6 + - + +
572B SER* 4.4 7.4 - - - +
574B GLU* 4.3 7.0 + - - +
581B TRP* 4.4 16.2 - - + -
582B GLY 2.6 25.3 + - - +
584B GLY* 1.3 71.2 - - - +
586B ASP* 1.3 63.4 + - - +
588B TRP* 3.3 11.8 + - - +
589B SER* 3.3 3.5 + - - -
694B ARG* 3.9 8.6 - - - +
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Residues in contact with ASP 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 4.1 11.5 - - + +
285B HIS* 2.9 28.7 - - - +
291B ILE* 3.4 5.3 - - - +
292B HIS* 2.8 34.1 + - - +
293B THR* 2.9 28.5 + - - -
295B ILE* 3.9 8.8 + - + +
566B GLN* 5.1 0.3 + - - -
583B CYS 2.8 11.8 + - - +
585B ALA* 1.3 75.9 - - - +
587B ILE* 1.3 59.2 + - - +
589B SER* 3.2 9.2 + - - -
590B THR* 2.9 31.7 + - - -
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Residues in contact with ILE 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 5.3 2.7 - - + -
281B LEU* 4.6 8.1 - - + -
285B HIS* 4.3 11.7 - - + +
583B CYS 4.5 0.2 - - - +
584B GLY* 2.9 10.5 + - - +
586B ASP* 1.3 75.3 - - - +
588B TRP* 1.3 66.6 + - - +
590B THR* 3.2 5.7 + - - +
591B ALA* 3.1 21.0 + - - +
686B MET* 3.6 35.5 - - + +
694B ARG* 3.9 4.9 - - + -
695B ALA 3.4 20.0 - - - +
697B ALA* 3.7 32.5 - - + +
700B LEU* 4.5 2.2 - - + -
732B TRP* 3.4 30.5 - - + -
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Residues in contact with TRP 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B TYR 3.6 5.4 - - - -
571B ARG 2.9 18.6 + - - -
572B SER* 3.3 25.1 - - - -
573B PRO* 3.4 37.0 - - + -
584B GLY 3.2 2.6 + - - -
585B ALA 3.4 10.1 - - - +
586B ASP 3.2 0.2 - - - -
587B ILE* 1.3 78.4 - - - +
589B SER* 1.3 64.1 + - - +
591B ALA* 3.2 13.6 + - - +
592B CYS* 3.2 25.6 + - - -
604B PHE* 3.3 28.8 - + - -
622B ILE* 4.0 11.4 - - + -
626B LEU* 3.6 21.8 - - + -
686B MET 3.8 8.7 - - - -
687B LEU* 3.2 42.4 - - + -
688B GLN 4.1 2.2 - - - -
689B LEU* 4.2 3.8 - - + -
694B ARG* 3.7 19.2 - - - +
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Residues in contact with SER 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.6 36.2 + - - +
566B GLN* 2.8 29.5 + - - +
570B TYR* 2.8 22.7 + - - +
585B ALA 3.3 1.4 + - - -
586B ASP* 3.2 10.1 + - - -
588B TRP* 1.3 79.2 - - - +
590B THR* 1.3 57.5 + - - +
592B CYS* 3.1 5.0 + - - +
593B LEU* 2.8 28.2 + - - +
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Residues in contact with THR 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 3.2 26.2 - - + +
278B LEU* 4.0 18.4 - - + -
281B LEU* 3.1 21.6 - - - +
295B ILE* 4.0 7.2 - - - +
586B ASP 2.9 13.6 + - - -
587B ILE* 3.2 12.3 + - - -
589B SER* 1.3 76.1 - - - +
591B ALA* 1.3 58.3 + - - +
593B LEU* 3.1 6.1 + - - +
594B ILE* 2.8 51.8 + - + +
686B MET* 4.3 4.0 - - - -
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Residues in contact with ALA 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B ILE 3.1 6.2 + - - +
588B TRP 3.4 9.9 - - - +
590B THR* 1.3 75.5 - - - +
592B CYS* 1.3 64.1 + - - +
594B ILE* 3.4 1.7 + - - +
595B PHE* 3.0 24.7 + - - +
603B LEU* 4.9 0.8 - - - +
683B LEU* 4.3 13.2 - - + +
686B MET* 3.5 37.4 - - + -
687B LEU* 3.6 26.2 - - + -
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Residues in contact with CYS 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B GLU 3.7 16.6 - - - +
570B TYR* 3.8 18.5 - - + -
588B TRP* 3.2 37.3 + - - -
589B SER 3.1 8.2 + - - +
591B ALA* 1.3 78.3 - - - +
593B LEU* 1.3 62.9 + - - +
595B PHE* 3.5 2.4 + - - +
596B GLU* 3.0 24.1 + - - +
603B LEU* 4.1 22.1 + - + +
604B PHE* 3.8 20.9 - - - -
687B LEU* 4.5 0.9 - - - -
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Residues in contact with LEU 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 4.3 5.6 - - + -
273B ILE* 6.1 0.4 - - + -
277B LEU* 4.7 9.9 - - + -
295B ILE* 4.0 17.7 - - + -
296B LYS 3.9 20.2 - - - -
297B PRO* 3.7 29.2 - - + -
300B VAL* 4.1 16.4 - - + -
570B TYR* 4.1 11.6 - - + -
589B SER 2.8 13.2 + - - +
590B THR* 3.4 9.2 - - - +
592B CYS* 1.3 75.6 - - - +
594B ILE* 1.3 63.2 + - + +
596B GLU* 3.1 6.8 + - + +
597B LEU* 2.9 47.9 + - + +
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Residues in contact with ILE 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 4.2 4.9 - - + -
273B ILE* 6.2 0.2 - - + -
274B SER* 3.4 41.1 - - - +
277B LEU* 5.3 2.2 - - + -
278B LEU* 5.2 0.9 - - + -
590B THR* 2.8 43.7 + - + +
591B ALA 3.9 3.1 - - - +
593B LEU* 1.3 74.4 - - + +
595B PHE* 1.3 64.4 + - - +
597B LEU* 2.9 15.1 + - + +
598B ILE* 2.9 37.9 + - + +
682B PHE* 4.1 18.8 - - + -
683B LEU* 3.9 16.2 - - + -
686B MET* 4.3 9.6 - - + -
705B TRP* 4.6 1.1 - - + -
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Residues in contact with PHE 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B ALA 3.0 17.6 + - - +
592B CYS 3.6 4.7 - - - +
594B ILE* 1.3 76.8 - - - +
596B GLU* 1.3 61.5 + - - +
598B ILE* 3.3 6.4 + - + +
599B THR* 2.8 60.9 + - + -
601B ASP 3.6 4.7 - - - -
602B PHE 3.8 7.6 - - - -
603B LEU* 3.4 57.7 - - + -
661B LEU* 3.8 21.5 - - + -
664B VAL* 4.4 7.9 - - + -
665B LEU* 4.1 12.8 - - + -
669B TYR* 3.9 19.1 - + - -
683B LEU* 4.4 17.0 - - + +
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Residues in contact with GLU 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LEU* 4.9 4.5 - - - +
257B ILE* 3.4 31.8 - - + +
262B HIS* 5.5 3.3 + - - -
297B PRO* 4.1 5.3 - - - +
570B TYR* 2.4 38.6 + - - -
592B CYS 3.0 12.3 + - - +
593B LEU* 3.1 9.6 + - - +
595B PHE* 1.3 78.4 - - - +
597B LEU* 1.3 56.0 + - - +
600B GLY* 2.7 37.3 + - - +
601B ASP 3.1 27.1 - - - +
602B PHE* 3.5 21.7 - - - -
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Residues in contact with LEU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LEU* 4.2 13.2 - - + -
257B ILE* 3.8 21.5 - - + -
264B GLY* 3.8 1.2 - - - -
265B ILE* 2.9 55.4 + - + +
270B VAL* 4.0 23.3 - - + +
273B ILE* 3.7 34.5 - - + -
593B LEU* 2.9 35.1 + - + +
594B ILE* 2.9 18.6 + - + +
596B GLU* 1.3 78.1 - - - +
598B ILE* 1.3 59.1 + - - +
600B GLY* 5.0 0.2 - - - -
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Residues in contact with ILE 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ARG 4.6 0.7 - - - +
264B GLY* 3.3 16.6 - - - -
265B ILE 3.9 4.9 + - - +
267B LEU* 4.0 13.9 - - + -
270B VAL* 3.9 19.5 - - + -
594B ILE* 2.9 28.7 + - + +
595B PHE* 3.7 7.0 - - + +
597B LEU* 1.3 77.4 - - - +
599B THR* 1.3 63.2 + - + +
665B LEU* 5.3 3.1 - - + -
671B PHE* 3.4 37.3 - - + -
679B ILE* 4.1 22.7 - - + -
683B LEU* 4.6 4.7 - - + -
705B TRP* 3.7 23.8 - - + -
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Residues in contact with THR 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B HIS 3.5 3.3 - - - +
263B ARG* 3.3 19.3 - - - +
264B GLY* 3.8 2.5 - - - -
595B PHE* 2.8 39.7 + - + +
598B ILE* 1.3 89.1 - - + +
600B GLY* 1.3 57.0 + - - +
601B ASP* 3.2 23.7 + - - +
665B LEU* 4.6 4.0 - - + -
669B TYR* 3.5 54.6 - - + -
671B PHE* 4.9 0.7 - - + -
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Residues in contact with GLY 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.6 5.3 - - - +
262B HIS* 3.2 54.9 - - - +
264B GLY* 3.9 5.1 - - - -
596B GLU* 2.7 27.8 + - - +
597B LEU 5.0 0.2 - - - -
598B ILE 3.8 0.4 - - - -
599B THR* 1.3 72.5 - - - +
601B ASP* 1.3 60.8 + - - +
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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