Contacts of the helix formed by residues 585 - 604 (chain B) in PDB entry 4HXG
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 SER 585 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASN* 3.2 29.1 + - - -
41B TYR* 4.3 3.6 - - - -
584B GLY* 1.3 73.6 - - - +
586B PRO* 1.3 64.4 - - - +
587B ARG* 5.1 1.0 + - - -
588B HIS* 3.1 25.6 + - - +
589B ARG* 2.7 33.8 + - - +
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Residues in contact with PRO 586 (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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11B PHE* 3.4 18.6 - - + -
12B THR* 4.9 0.7 - - + -
34B ALA* 4.1 17.0 - - + -
35B ASN 3.6 31.4 - - - +
36B LEU* 3.6 15.0 - - + -
39B ASN* 3.0 21.3 - - - +
40B LYS* 3.8 14.4 - - - +
41B TYR* 4.2 14.4 - - + +
584B GLY 3.8 0.4 - - - +
585B SER* 1.3 83.8 - - - +
587B ARG* 1.3 56.2 - - - +
589B ARG* 4.5 0.4 - - + -
590B MET* 2.9 29.6 + - - +
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Residues in contact with ARG 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.6 18.4 - - + +
39B ASN* 3.0 55.8 + - + +
585B SER* 5.1 1.8 + - - -
586B PRO* 1.3 76.4 - - - +
588B HIS* 1.3 63.5 + - - +
590B MET* 3.2 10.1 + - + +
591B LYS* 3.0 57.9 + - - +
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Residues in contact with HIS 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B PHE* 3.2 35.1 - + + +
575B LYS* 3.1 35.4 + - - +
576B GLY* 4.6 0.2 - - - -
580B HIS* 3.1 42.9 + - + +
584B GLY* 4.4 3.5 - - - -
585B SER* 3.1 29.9 + - - +
587B ARG* 1.3 77.1 - - - +
589B ARG* 1.3 73.7 + - + +
590B MET 3.0 0.7 + - - -
591B LYS* 3.2 7.1 + - - -
592B ARG* 3.1 20.5 + - + +
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Residues in contact with ARG 589 (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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11B PHE* 3.4 42.8 - - + +
16B TYR* 4.7 12.7 + - - -
34B ALA* 5.1 1.0 - - - +
41B TYR* 3.2 32.1 + - - -
398B TYR* 5.6 1.4 - - - +
580B HIS 3.6 10.1 - - - +
581B SER 2.8 24.5 + - - +
582B ILE* 3.2 30.6 + - - +
584B GLY 3.4 7.6 - - - +
585B SER 2.7 20.0 + - - +
586B PRO 3.7 3.6 - - - +
588B HIS* 1.3 78.0 - - - +
590B MET* 1.3 63.3 + - - +
592B ARG* 3.3 5.6 + - - +
593B TYR* 3.0 52.0 + - + -
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Residues in contact with MET 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 3.5 32.3 - - + +
9B LYS* 4.2 21.1 - - + -
11B PHE* 4.0 13.9 - - + -
36B LEU* 4.1 24.9 - - + -
586B PRO 2.9 15.5 + - - +
587B ARG* 3.4 15.5 - - + +
588B HIS 3.0 0.4 - - - -
589B ARG* 1.3 76.0 - - - +
591B LYS* 1.3 96.2 + - + +
593B TYR* 3.0 6.7 + - - +
594B LYS* 2.9 20.9 + - + +
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Residues in contact with LYS 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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573B PHE* 4.6 11.9 - - + -
587B ARG* 3.0 43.5 + - + +
588B HIS* 3.8 6.5 - - - +
590B MET* 1.3 90.7 - - + +
592B ARG* 1.3 66.6 + - - +
594B LYS* 3.0 8.4 + - - +
595B LEU* 2.8 25.1 + - - +
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Residues in contact with ARG 592 (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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397B LYS* 5.5 0.2 - - - +
399B GLU* 2.9 32.5 + - - +
465B ILE* 4.2 7.1 - - - +
488B GLU* 2.6 41.9 + - - -
541B ILE* 4.3 14.1 - - + +
573B PHE* 3.7 23.1 - - + -
580B HIS* 4.4 14.1 - - - -
581B SER* 3.4 34.4 + - - +
588B HIS* 3.1 12.1 + - + +
589B ARG* 3.5 9.6 + - - +
591B LYS* 1.3 75.2 - - - +
593B TYR* 1.3 78.8 + - - +
595B LEU* 2.9 7.6 + - - +
596B PHE* 2.7 44.8 + - + +
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Residues in contact with TYR 593 (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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8B GLU* 3.7 17.7 - - - -
11B PHE* 3.6 36.1 - + - -
398B TYR* 3.4 40.9 - + + +
399B GLU* 3.4 20.8 + - + -
402B LEU* 4.8 8.5 - - + +
581B SER 3.8 9.8 + - - -
582B ILE* 4.8 4.9 - - - +
589B ARG* 3.0 44.5 + - + -
590B MET 3.0 7.0 + - - +
592B ARG* 1.3 106.2 - - - +
594B LYS* 1.3 63.2 + - - +
596B PHE* 3.1 6.2 + - + +
597B MET* 2.9 27.8 + - - +
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Residues in contact with LYS 594 (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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8B GLU* 3.2 41.5 + - + +
590B MET* 2.9 15.8 + - + +
591B LYS* 3.5 10.8 - - - +
593B TYR* 1.3 73.2 - - - +
595B LEU* 1.3 57.3 + - - +
597B MET* 3.5 15.0 - - + +
598B GLU* 2.7 66.5 + - + +
616B ILE 3.6 19.2 + - - -
617B LEU* 4.0 26.7 - - + +
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Residues in contact with LEU 595 (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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539B LEU* 4.2 16.9 - - + +
541B ILE* 4.6 12.1 - - + -
571B ALA* 3.7 28.9 - - + -
573B PHE* 4.5 18.6 - - + -
591B LYS 2.8 11.3 + - - +
592B ARG 3.2 7.4 - - - +
594B LYS* 1.3 76.2 - - - +
596B PHE* 1.3 67.1 + - - +
598B GLU* 3.6 2.7 + - - +
599B PHE* 3.2 22.5 + - - +
611B PHE* 3.7 29.6 - - + -
613B VAL* 4.5 15.0 - - + -
617B LEU* 6.5 1.1 - - + -
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Residues in contact with PHE 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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383B PHE* 4.1 16.8 - + - -
399B GLU* 4.1 24.7 - - + -
402B LEU* 5.4 2.7 - - + -
403B MET* 3.9 31.2 - - + -
463B THR* 3.6 25.6 - - + -
486B ILE* 3.8 22.8 - - + +
488B GLU* 3.9 19.5 - - - -
539B LEU* 5.3 2.0 - - - -
541B ILE* 5.2 3.8 - - + +
592B ARG* 2.7 32.5 + - + +
593B TYR* 3.3 14.1 - + - +
595B LEU* 1.3 75.1 - - - +
597B MET* 1.3 66.3 + - + +
598B GLU 3.3 0.2 + - - -
599B PHE* 3.4 8.7 + - - +
600B PHE* 3.5 26.7 + + - -
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Residues in contact with MET 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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6B TRP 5.0 0.2 - - - +
7B ASP* 4.5 4.3 - - - -
8B GLU* 3.8 23.1 - - + +
402B LEU* 3.6 33.7 - - + -
403B MET* 4.0 13.3 - - - +
406B LYS* 3.4 42.2 - - + +
593B TYR 2.9 9.8 + - - +
594B LYS* 3.5 37.7 - - + +
596B PHE* 1.3 80.3 - - - +
598B GLU* 1.3 66.6 + - - +
600B PHE* 3.3 4.9 + - - +
601B GLU* 3.2 23.7 + - + +
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Residues in contact with GLU 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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594B LYS* 2.7 53.9 + - + +
595B LEU* 4.2 1.8 - - - +
597B MET* 1.3 83.0 - - + +
599B PHE* 1.3 66.5 + - - +
601B GLU* 3.2 11.7 + - - +
602B ARG* 2.9 45.6 + - - +
611B PHE* 4.0 9.2 - - + -
616B ILE* 3.4 37.2 - - + +
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Residues in contact with PHE 599 (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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484B ALA* 4.8 1.1 - - + -
485B GLY 3.6 24.2 - - - -
486B ILE* 3.6 24.0 - - + -
537B PRO 4.2 6.5 - - - -
538B LEU 3.7 12.3 - - - -
539B LEU* 3.5 34.8 - - + -
569B TYR* 3.8 22.7 - + - -
595B LEU 3.2 17.5 + - - +
596B PHE 3.8 3.6 - - - +
597B MET 3.3 0.2 - - - -
598B GLU* 1.3 76.3 - - - +
600B PHE* 1.3 58.9 + + - +
603B LYS* 2.6 71.1 + - + +
611B PHE* 3.6 26.4 - + + -
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Residues in contact with PHE 600 (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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381B ILE* 3.9 28.3 - - + -
403B MET* 3.9 12.6 - - + -
408B TYR* 3.3 7.7 + - + +
461B GLY* 4.2 13.0 - - - -
462B ILE 4.5 6.7 - - - -
463B THR* 4.1 14.8 - - - -
484B ALA* 4.7 12.3 - - + -
486B ILE* 3.5 39.7 - - + -
596B PHE* 3.5 30.4 + + - -
597B MET 3.3 8.1 + - - +
599B PHE* 1.3 79.1 - + - +
601B GLU* 1.3 60.2 + - - +
604B LEU* 2.8 54.0 + - + +
605B LYS 2.9 10.7 + - - -
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Residues in contact with GLU 601 (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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406B LYS* 3.8 21.4 + - - -
408B TYR* 2.5 37.3 + - + +
597B MET 3.2 18.3 + - - +
598B GLU* 3.2 18.6 + - - +
600B PHE* 1.3 76.5 - - - +
602B ARG* 1.3 61.9 + - + +
605B LYS* 2.7 37.3 + - - +
606B LYS* 3.1 30.7 + - - +
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Residues in contact with ARG 602 (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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598B GLU* 2.9 34.3 + - - +
599B PHE 4.1 0.9 - - - +
601B GLU* 1.3 80.7 - - + +
603B LYS* 1.3 60.0 + - + +
606B LYS 2.9 18.8 - - - +
607B TYR* 3.1 0.2 - - - -
608B GLU* 2.8 72.3 + - + +
610B GLY 5.4 0.7 - - - +
611B PHE* 4.1 13.2 - - + -
616B ILE* 3.5 48.8 - - - +
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Residues in contact with LYS 603 (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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483B LYS* 4.3 6.8 - - - +
484B ALA* 3.8 12.8 - - + +
537B PRO* 4.1 14.3 - - + +
567B GLU* 2.7 26.7 + - - +
569B TYR* 3.4 5.9 + - - -
599B PHE* 2.6 58.1 + - + +
602B ARG* 1.3 78.2 - - + +
604B LEU* 1.3 58.1 + - - +
607B TYR* 3.5 38.3 + - + +
608B GLU 2.7 24.2 + - - -
610B GLY 3.0 29.1 + - - +
611B PHE* 4.4 7.2 - - - -
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Residues in contact with LEU 604 (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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379B PRO* 4.5 7.0 - - + -
380B VAL 3.7 20.2 - - - +
381B ILE* 4.0 4.5 - - + -
408B TYR* 4.0 18.6 - - + -
459B ARG* 3.3 21.1 - - + +
460B ILE 3.7 16.8 - - - +
461B GLY* 3.5 25.4 - - - +
483B LYS* 4.2 15.4 - - + +
484B ALA* 4.2 6.3 - - + -
600B PHE* 2.8 49.8 + - + +
602B ARG 3.6 1.6 - - - -
603B LYS* 1.3 74.5 - - - +
605B LYS* 1.3 66.3 + - - +
606B LYS* 3.5 1.6 - - - -
607B TYR* 4.7 1.4 + - - +
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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