Contacts of the helix formed by residues 584 - 599 (chain G) in PDB entry 1H1V
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 584 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543G ALA* 4.9 0.9 - - - +
582G GLY 3.3 5.6 + - - -
583G ALA* 1.3 73.8 - - - +
585G GLU* 1.3 64.8 + - - +
586G ALA* 3.6 14.7 + - - +
587G GLU* 3.1 30.1 + - - +
588G LYS* 2.9 25.0 + - - +
633G LYS* 6.2 0.9 - - - -
636G ASP* 4.9 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 585 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G SER* 1.3 72.9 - - - +
586G ALA* 1.3 54.1 + - - +
588G LYS* 2.5 56.3 + - - +
589G THR* 2.7 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 586 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543G ALA* 3.9 21.1 - - + -
544G ASN 5.8 0.2 - - - +
547G GLY* 4.1 15.9 - - - +
549G THR* 3.8 12.9 + - - +
584G SER* 3.3 6.8 + - - +
585G GLU* 1.3 78.2 - - - +
587G GLU* 1.3 57.7 + - - +
589G THR* 3.5 8.1 + - - +
590G GLY* 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 587 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G VAL* 3.3 26.3 - - - +
542G ARG* 3.6 2.5 - - - -
543G ALA* 3.3 32.9 + - + +
549G THR* 4.6 1.3 - - - -
564G ASN 3.0 6.2 - - - +
565G ASP* 2.7 22.6 - - - +
566G ALA* 3.6 11.8 - - + +
583G ALA* 4.2 1.6 - - + -
584G SER* 3.1 29.2 + - - +
585G GLU 3.1 0.6 - - - -
586G ALA* 1.3 73.2 - - - +
588G LYS* 1.3 64.9 + - - +
591G ALA* 2.9 25.1 + - - +
1745G CA 2.5 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 588 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566G ALA* 4.7 3.4 - - - -
577G LEU* 5.0 3.7 - - - +
579G VAL* 3.9 32.4 - - + +
583G ALA* 4.6 8.9 + - + +
584G SER 2.9 20.9 + - - +
585G GLU* 2.5 49.9 + - - +
587G GLU* 1.3 70.7 - - - +
589G THR* 1.3 66.2 + - - +
591G ALA* 3.1 19.7 - - - +
592G GLN* 3.2 12.5 + - - +
633G LYS* 5.8 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 589 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514G GLY 5.4 7.2 - - - +
516G PRO* 6.3 0.2 - - + -
585G GLU* 2.7 17.2 + - - +
586G ALA* 3.6 11.2 - - - +
588G LYS* 1.3 71.1 - - - +
590G GLY* 1.3 59.4 + - - +
592G GLN* 2.7 36.1 + - - +
593G GLU* 3.0 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 590 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G PRO* 3.7 23.5 - - - +
541G VAL* 4.1 8.0 - - - +
549G THR* 4.4 6.5 - - - -
551G ALA* 5.4 0.2 - - - +
586G ALA 2.9 15.1 + - - -
587G GLU 4.3 0.4 - - - -
589G THR* 1.3 80.6 - - - +
591G ALA* 1.3 61.1 + - - +
593G GLU* 3.8 10.3 - - - -
594G LEU* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 591 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541G VAL* 3.9 14.6 - - + +
566G ALA* 4.1 11.7 - - + -
568G VAL* 3.3 24.9 - - + +
577G LEU* 4.0 24.2 - - + -
587G GLU 2.9 22.2 + - - +
588G LYS 3.1 9.2 - - - +
589G THR 2.9 0.6 + - - -
590G GLY* 1.3 76.6 - - - +
592G GLN* 1.3 63.4 + - - +
594G LEU* 3.5 2.1 + - - +
595G LEU* 3.4 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 592 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G LEU* 3.5 19.1 - - + -
588G LYS 3.9 9.2 - - - +
589G THR* 2.7 15.8 + - - +
591G ALA* 1.3 74.4 - - - +
593G GLU* 1.3 56.5 + - - +
594G LEU 2.9 1.3 - - - -
595G LEU* 2.5 36.0 + - + +
596G ARG* 3.1 36.7 + - + +
602G PRO* 5.7 0.7 - - + -
604G GLN* 3.4 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 593 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514G GLY 5.6 0.4 - - - +
515G LYS* 2.8 42.2 + - - +
516G PRO* 3.4 29.8 - - + -
589G THR* 3.0 23.4 + - + +
590G GLY* 3.8 5.8 - - - +
592G GLN* 1.3 75.8 - - - +
594G LEU* 1.3 57.7 + - - +
596G ARG* 3.5 37.7 + - - +
597G VAL* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 594 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516G PRO* 4.7 0.2 - - - +
518G ILE* 3.5 34.8 - - + -
520G TYR* 5.0 2.2 - - + -
539G PHE* 4.1 40.2 - - + -
541G VAL* 5.3 1.3 - - + -
551G ALA* 4.5 9.0 - - + -
568G VAL* 3.3 43.3 - - + -
590G GLY 3.2 17.0 + - - +
591G ALA* 3.7 4.5 - - - +
592G GLN 2.7 2.2 + - - -
593G GLU* 1.3 72.4 - - - +
595G LEU* 1.3 66.1 + - - +
597G VAL* 3.6 4.4 - - + +
598G LEU* 3.3 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 595 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568G VAL* 3.5 26.9 - - + -
570G LYS* 5.7 4.3 - - + -
575G ALA* 5.5 5.8 - - + -
576G TYR 4.6 5.2 - - - +
577G LEU* 3.5 27.1 - - + -
591G ALA 3.4 8.5 + - - +
592G GLN* 2.5 16.9 + - + +
594G LEU* 1.3 71.0 - - - +
596G ARG* 1.3 57.0 + - + +
599G ARG* 2.6 38.6 + - - -
600G ALA* 3.8 23.1 + - + +
601G GLN* 5.8 0.7 - - - +
602G PRO* 2.8 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 596 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592G GLN* 3.1 30.5 + - + +
593G GLU* 3.7 43.6 + - - +
595G LEU* 1.3 79.3 - - + +
597G VAL* 1.3 69.1 + - - +
598G LEU 2.7 2.8 + - - -
599G ARG* 2.9 21.7 + - - +
600G ALA 5.1 2.5 - - - -
601G GLN* 5.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440G GLN* 3.9 23.3 - - + +
515G LYS* 6.1 4.7 - - + -
516G PRO* 6.1 1.6 - - + -
518G ILE* 3.8 28.3 - - + -
520G TYR* 3.9 13.2 - - - +
593G GLU* 3.0 25.7 + - + +
594G LEU* 3.6 6.1 - - + +
596G ARG* 1.3 80.6 - - + +
598G LEU* 1.3 72.4 + - + +
599G ARG* 4.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 598 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520G TYR* 3.9 32.1 - - + +
533G PRO* 6.5 0.9 - - + -
537G ARG* 4.9 11.9 - - - +
570G LYS* 3.2 15.7 + - + +
594G LEU* 3.3 13.0 + - + +
596G ARG 2.7 3.0 + - - -
597G VAL* 1.3 89.8 - - + +
599G ARG* 1.3 83.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 599 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570G LYS* 2.7 30.0 + - - +
595G LEU* 2.6 19.2 + - - -
596G ARG* 2.9 13.1 + - - +
597G VAL 4.3 6.6 + - - -
598G LEU* 1.3 93.1 - - + +
600G ALA* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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