Contacts of the helix formed by residues 569 - 588 (chain D) in PDB entry 2HVH
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 GLU 569 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517D ARG* 3.1 36.5 + - - -
521D LEU* 3.8 13.5 - - + +
565D ALA 4.8 1.5 + - - -
568D HIS* 1.3 77.4 + - + +
570D ILE* 1.3 63.6 + - - +
571D VAL 3.1 1.4 + - - -
572D GLU* 3.5 15.8 + - - +
573D ASN* 3.0 22.2 + - - +
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Residues in contact with ILE 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D ILE* 3.4 37.9 - - + +
521D LEU* 3.8 20.4 - - + +
522D ALA* 3.5 27.4 - - + +
526D PHE* 5.5 0.7 - - + -
537D ILE* 5.2 3.8 - - + -
538D LEU* 3.9 25.6 - - + -
542D LEU* 4.0 10.5 - - + -
568D HIS* 3.1 27.0 + - + +
569D GLU* 1.3 76.7 - - - +
571D VAL* 1.3 62.0 + - + +
572D GLU 3.5 0.2 - - - -
573D ASN* 3.3 4.2 + - - +
574D ILE* 3.0 35.1 + - + +
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Residues in contact with VAL 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D LEU* 4.6 6.7 - - + -
544D LEU* 4.2 19.7 - - + -
561D LEU* 3.5 34.4 - - + +
564D LEU* 4.1 23.3 - - + -
565D ALA* 3.6 23.6 - - + +
568D HIS 3.3 16.4 + - - +
570D ILE* 1.3 78.6 - - + +
572D GLU* 1.3 70.8 + - + +
574D ILE* 3.0 11.1 + - + +
575D LEU* 3.0 27.1 + - - +
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Residues in contact with GLU 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D GLU* 6.5 0.9 - - - -
565D ALA* 4.5 24.1 - - + +
569D GLU* 3.5 10.8 + - - +
570D ILE 3.5 0.2 - - - -
571D VAL* 1.3 79.6 - - + +
573D ASN* 1.3 62.1 + - - +
575D LEU* 3.6 14.8 + - + +
576D HIS* 3.1 23.7 + - - +
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Residues in contact with ASN 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514D VAL* 3.6 13.6 - - + +
517D ARG* 3.4 27.8 + - - +
518D ILE* 3.8 18.6 - - + -
521D LEU* 3.7 7.8 - - - +
569D GLU* 3.0 41.6 + - - +
570D ILE* 3.3 9.6 + - + +
571D VAL 3.1 0.6 - - - -
572D GLU* 1.3 77.3 - - - +
574D ILE* 1.3 58.5 + - - +
576D HIS* 3.5 4.4 + - - +
577D TYR* 2.9 28.8 + - - +
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Residues in contact with ILE 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518D ILE* 3.9 23.6 - - + -
526D PHE* 5.4 0.7 - - + -
528D ILE* 4.3 13.5 - - + -
534D LEU* 3.7 39.5 - - + -
538D LEU* 4.2 10.3 - - + -
561D LEU* 3.8 19.1 - - + -
570D ILE* 3.0 42.5 + - + +
571D VAL* 3.0 10.5 + - - +
573D ASN* 1.3 73.2 - - - +
575D LEU* 1.3 66.1 + - - +
577D TYR* 3.0 4.3 + - - +
578D ARG* 2.8 32.5 + - + +
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Residues in contact with LEU 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D ALA* 3.9 22.4 - - + -
561D LEU* 4.0 23.6 - - + +
562D GLU* 3.7 34.1 - - + +
571D VAL 3.0 17.2 + - - +
572D GLU* 3.8 16.8 - - + +
574D ILE* 1.3 77.2 - - - +
576D HIS* 1.3 64.1 + - - +
578D ARG* 3.1 5.0 + - - +
579D GLN* 3.1 35.6 + - - +
26E C 3.7 21.3 + - - +
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Residues in contact with HIS 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D GLN* 4.3 8.3 - - - -
514D VAL* 4.0 20.6 - - + +
572D GLU 3.1 16.4 + - - +
573D ASN* 3.6 7.0 - - - +
575D LEU* 1.3 77.5 - - - +
577D TYR* 1.3 62.4 + - - +
579D GLN* 3.2 21.6 - - + +
580D LEU* 3.1 46.7 + - + +
632D GLU* 3.5 27.4 + - - -
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Residues in contact with TYR 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LEU* 3.8 44.2 - - + +
514D VAL* 3.8 10.4 - - + +
515D GLU* 4.1 27.0 - - + +
518D ILE* 3.8 9.4 - - + -
528D ILE* 3.7 38.0 + - + +
529D ASN* 3.6 33.8 + - - -
573D ASN 2.9 14.7 + - - +
574D ILE* 3.0 7.4 + - - +
576D HIS* 1.3 76.3 - - - +
578D ARG* 1.3 62.3 + - + +
580D LEU* 3.3 6.8 + - - +
581D GLY* 2.9 28.4 + - - -
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Residues in contact with ARG 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ILE 4.3 15.2 + - - +
529D ASN* 4.4 13.0 - - - +
531D PRO* 5.1 5.1 - - - +
534D LEU* 3.5 17.9 - - - +
556D THR* 2.5 47.7 + - - -
557D SER 4.2 2.4 - - - -
561D LEU* 3.7 14.7 - - - +
574D ILE* 2.8 28.7 + - + +
575D LEU* 3.1 3.2 + - - +
577D TYR* 1.3 85.2 - - + +
579D GLN* 1.3 56.8 + - - +
581D GLY* 3.6 2.0 + - - +
582D LYS* 3.2 22.7 + - - +
25E A 3.0 32.2 + - + -
26E C 3.0 40.2 + - - +
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Residues in contact with GLN 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575D LEU* 3.1 21.0 + - - +
576D HIS* 3.2 37.2 - - + +
578D ARG* 1.3 75.6 - - - +
580D LEU* 1.3 66.6 + - + +
581D GLY 3.0 1.8 - - - -
582D LYS* 3.2 4.1 + - - +
583D LEU* 3.1 28.7 + - + +
630D LEU* 3.7 27.8 - - + +
26E C 3.7 13.0 - - - +
27E T 3.4 26.2 + - - +
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Residues in contact with LEU 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LEU* 3.9 22.0 - - + +
510D GLN* 3.9 31.0 - - + +
511D LEU* 3.6 26.9 - - + +
514D VAL* 4.4 10.1 - - + -
576D HIS* 3.1 40.5 + - + +
577D TYR* 3.8 0.4 - - - +
579D GLN* 1.3 79.2 - - + +
581D GLY* 1.3 59.8 + - - +
583D LEU* 3.7 14.5 + - + +
584D GLN* 3.3 22.5 + - - +
632D GLU* 3.5 29.6 - - + +
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Residues in contact with GLY 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511D LEU* 4.4 13.5 - - - -
529D ASN* 5.8 4.5 - - - -
577D TYR* 2.9 21.9 + - - -
578D ARG* 4.0 3.8 - - - -
579D GLN 3.0 0.4 - - - -
580D LEU* 1.3 76.1 - - - +
582D LYS* 1.3 59.3 + - - +
584D GLN* 3.6 2.6 + - - +
585D SER* 2.9 32.0 + - - -
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Residues in contact with LYS 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578D ARG 3.2 13.5 + - - +
579D GLN* 3.2 11.8 + - - +
581D GLY* 1.3 74.7 - - - +
583D LEU* 1.3 60.0 + - - +
585D SER* 3.3 5.0 + - - +
586D THR* 2.8 67.6 + - - +
587D TYR* 4.2 13.7 - - + -
25E A 4.4 5.1 - - + +
26E C 3.5 45.6 + - + +
27E T 4.3 9.0 - - - +
7F G 4.1 7.1 - - - +
8F T 2.5 31.3 + - - -
9F C 3.8 7.9 + - - -
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Residues in contact with LEU 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D LEU* 3.7 28.5 - - + -
579D GLN* 3.1 16.2 + - + +
580D LEU* 3.9 13.9 - - + +
582D LYS* 1.3 78.6 - - - +
584D GLN* 1.3 58.7 + - - +
587D TYR* 2.9 34.6 + - + -
588D ILE* 3.1 12.8 + - - +
627D PRO* 3.6 23.1 - - + -
632D GLU* 4.1 8.3 - - + +
633D GLY* 3.6 37.9 - - - +
636D ILE* 4.3 12.6 - - + -
27E T 5.4 5.8 - - - -
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Residues in contact with GLN 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504D GLY* 4.3 6.1 - - - +
507D LEU* 3.6 14.0 - - + +
508D ALA* 3.5 27.7 + - - +
511D LEU* 3.4 28.0 - - + +
580D LEU 3.3 15.0 + - - +
581D GLY* 4.0 3.3 + - - +
582D LYS 3.3 0.2 - - - -
583D LEU* 1.3 81.1 - - - +
585D SER* 1.3 58.7 + - - +
588D ILE* 3.4 9.6 - - + +
589D GLU* 3.0 52.9 + - + +
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Residues in contact with SER 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D GLY 2.9 22.3 + - - -
582D LYS* 3.3 9.5 + - - +
584D GLN* 1.3 79.9 - - - +
586D THR* 1.3 65.3 + - - +
589D GLU* 3.6 14.8 - - - +
590D GLY* 3.4 14.2 + - - -
9F C 3.5 32.4 + - - +
10F A 4.1 18.9 + - - -
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Residues in contact with THR 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D LYS* 2.8 50.6 + - - +
585D SER* 1.3 77.3 + - - +
587D TYR* 1.3 82.3 + - + +
588D ILE 3.4 2.0 - - - -
590D GLY* 3.3 5.1 - - - +
591D LEU* 3.3 22.2 + - - +
625D ASN* 6.1 0.9 - - - +
7F G 6.1 0.4 - - - +
8F T 4.1 26.2 - - - +
9F C 3.4 14.6 - - - +
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Residues in contact with TYR 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D LEU* 3.7 9.0 - - - +
582D LYS* 4.0 12.6 - - + -
583D LEU* 2.9 28.9 + - + +
586D THR* 1.3 95.2 - - + +
588D ILE* 1.3 60.3 + - - +
591D LEU* 3.8 18.8 - - + +
622D ASN 5.2 1.3 - - - -
625D ASN* 2.7 44.6 + - - -
626D ILE* 3.9 19.5 - - + -
627D PRO* 3.6 32.1 - - + -
636D ILE* 3.3 33.0 - - + +
27E T 3.3 28.4 + - - -
7F G 4.9 0.2 + - - -
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Residues in contact with ILE 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D LEU* 3.6 30.5 - - + +
501D GLU* 5.3 0.9 - - - -
503D MET* 4.2 8.3 - - + -
504D GLY* 3.8 26.7 - - - +
507D LEU* 4.3 9.0 - - + -
583D LEU 3.1 15.7 + - - +
584D GLN* 3.4 17.3 - - + +
587D TYR* 1.3 79.3 - - - +
589D GLU* 1.3 67.7 + - + +
590D GLY 3.3 0.2 - - - -
591D LEU* 3.3 1.9 + - - +
592D LEU* 2.9 48.4 + - + +
636D ILE* 3.5 24.0 - - + -
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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