Contacts of the helix formed by residues 530 - 540 (chain A) in PDB entry 2HHT
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 530 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASN* 2.9 17.3 + - - -
528A ILE 3.0 3.1 - - - -
529A ASN* 1.3 79.9 - - - +
531A PRO* 1.3 66.5 - - - +
532A LYS* 3.0 4.5 + - - +
533A GLN* 3.3 26.7 + - - +
534A LEU* 2.8 25.6 + - - +
13C A 3.3 15.1 + - - -
14C T 2.6 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASN 3.3 12.1 - - - +
530A SER* 1.3 82.9 - - - +
532A LYS* 1.3 56.8 + - - +
534A LEU* 3.9 6.0 - - + +
535A GLY* 2.9 24.9 + - - -
554A TYR 4.8 7.7 + - - +
556A THR* 4.2 18.7 - - + +
578A ARG* 5.1 2.7 - - - +
25B A 3.9 40.8 - - - +
26B G 4.4 13.0 - - - +
12C G 6.1 3.4 - - - +
13C A 5.0 5.6 - - - +
14C T 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 3.0 7.9 + - - +
531A PRO* 1.3 78.3 - - - +
533A GLN* 1.3 68.4 + - + +
535A GLY* 3.2 2.6 + - - -
536A VAL* 3.2 27.6 + - + +
552A THR* 4.5 17.7 - - + +
553A GLY* 6.1 4.5 - - - -
554A TYR* 5.6 1.1 - - - +
14C T 4.4 19.5 + - - +
15C C 2.5 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A PHE* 3.8 16.1 - - + +
527A ASN* 2.9 50.0 + - - +
530A SER* 3.1 14.6 + - - +
532A LYS* 1.3 82.4 - - + +
534A LEU* 1.3 63.6 + - - +
536A VAL* 3.1 18.4 + - - +
537A ILE* 3.2 16.3 + - - +
14C T 3.6 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A PHE* 3.9 26.1 - - + -
528A ILE* 4.0 17.0 - - + +
530A SER 2.8 17.6 + - - +
531A PRO* 3.9 3.6 - - + +
533A GLN* 1.3 76.6 - - - +
535A GLY* 1.3 63.9 + - - +
537A ILE* 3.2 2.5 + - + +
538A LEU* 3.0 42.8 + - + +
556A THR* 4.1 11.9 - - + +
561A LEU* 5.2 0.4 - - + -
574A ILE* 3.4 44.0 - - + -
578A ARG* 3.3 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PRO 2.9 20.0 + - - -
532A LYS 3.2 2.9 + - - -
533A GLN 3.2 0.6 - - - -
534A LEU* 1.3 77.4 - - - +
536A VAL* 1.3 55.5 + - - +
539A PHE* 3.1 43.1 + - - +
554A TYR* 3.7 23.2 - - - -
556A THR* 4.4 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LYS* 3.2 21.1 + - + +
533A GLN* 3.1 10.4 + - - +
535A GLY* 1.3 73.0 - - - +
537A ILE* 1.3 68.1 + - + +
540A GLU* 3.0 57.7 + - + +
541A LYS* 3.0 10.9 + - + +
554A TYR* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ALA* 3.8 23.8 - - + -
524A GLN* 3.5 40.4 - - + +
526A PHE* 3.8 31.0 - - + -
533A GLN 3.2 12.8 + - - +
534A LEU 3.2 7.1 + - - +
536A VAL* 1.3 82.3 - - + +
538A LEU* 1.3 61.3 + - + +
541A LYS* 3.4 11.6 - - + +
542A LEU* 2.9 36.3 + - + +
570A ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 3.0 39.0 + - + +
537A ILE* 1.3 80.4 - - + +
539A PHE* 1.3 80.4 + - + +
542A LEU* 3.5 7.8 - - + +
543A GLN 3.3 8.0 + - - -
544A LEU* 2.9 43.9 + - + +
556A THR* 4.6 2.0 - - + -
561A LEU* 3.7 28.9 - - + -
564A LEU* 5.0 0.7 - - + -
570A ILE* 3.9 23.8 - - + -
571A VAL* 5.1 2.0 - - + -
574A ILE* 3.7 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLY* 3.1 22.5 + - - +
538A LEU* 1.3 85.7 - - + +
540A GLU* 1.3 63.3 + - - +
543A GLN* 4.1 14.1 + - - -
544A LEU* 3.5 23.5 - - + +
545A PRO 3.3 20.9 - - - -
546A VAL* 3.7 26.8 - - + +
547A LEU 5.3 0.4 - - - -
548A LYS 5.8 1.3 - - - -
554A TYR* 3.4 39.5 + + + -
555A SER 3.5 20.6 - - - -
556A THR* 4.0 14.6 - - + -
560A VAL* 4.6 3.4 - - + -
564A LEU* 3.6 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL* 3.0 37.5 + - + +
538A LEU 3.4 0.4 - - - -
539A PHE* 1.3 80.3 - - - +
541A LYS* 1.3 67.3 + - - +
542A LEU 3.4 0.7 - - - -
543A GLN* 2.7 28.6 + - - +
554A TYR* 2.7 35.4 + - + +
----------------------------------------------------------
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