Contacts of the strand formed by residues 551 - 555 (chain A) in PDB entry 1R1H
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 GLN 551 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LYS* 3.2 18.9 - - + +
478A ARG* 3.4 35.6 + - + +
531A LYS 5.0 0.7 - - - +
533A GLU 4.0 6.8 + - - +
534A TRP* 4.1 1.4 - - - +
535A ILE* 3.7 26.0 - - + +
544A PHE 3.9 0.3 - - - +
545A TYR* 3.3 7.6 - - - -
546A SER* 3.0 29.9 + - - -
549A ARG* 3.9 32.3 - - + +
550A ASN* 1.3 75.7 - - - +
552A ILE* 1.3 65.3 + - - +
553A VAL* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 3.9 23.3 - - + -
447A ARG* 5.5 1.1 - - - +
475A ILE* 3.6 21.9 - - + +
476A LYS 3.1 3.3 + - - +
477A GLU* 3.4 12.4 - - + -
478A ARG* 2.8 26.2 + - - +
544A PHE 3.4 3.8 - - - +
545A TYR* 3.8 16.8 - - + -
551A GLN* 1.3 74.5 - - - +
553A VAL* 1.3 66.0 + - - +
554A PHE* 3.5 28.9 - - + -
584A GLU* 3.7 27.1 - - + -
585A ILE* 3.9 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ARG* 3.4 7.2 - - + +
534A TRP* 3.9 26.7 - - + -
535A ILE* 3.4 20.4 - - + -
536A SER* 4.5 11.4 - - - +
543A ALA* 3.3 9.4 - - - +
544A PHE* 3.0 39.2 + - + +
551A GLN* 3.2 33.2 - - + +
552A ILE* 1.3 80.3 - - - +
554A PHE* 1.3 65.8 + - - +
555A PRO* 3.4 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 5.0 3.6 - - + -
443A ILE* 3.6 25.1 - - + -
478A ARG 2.8 16.7 + - - +
479A ILE* 4.7 2.9 - - + -
480A GLY 2.8 29.5 + - - -
543A ALA* 3.8 11.2 - - + -
552A ILE* 3.5 39.3 - - + -
553A VAL* 1.3 77.3 - - - +
555A PRO* 1.3 65.2 - - - +
558A ILE* 4.6 2.2 - - + -
559A LEU* 3.6 21.3 - - + +
577A ILE* 4.8 6.7 - - + -
580A VAL* 4.1 5.6 - - + -
581A ILE* 3.6 44.6 - - + -
584A GLU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLY 3.7 7.4 - - - +
534A TRP* 5.1 2.7 - - + -
536A SER* 3.6 24.9 - - - +
537A GLY 3.5 18.4 - - - +
538A ALA* 3.6 8.3 - - - +
540A VAL* 3.6 12.6 - - + +
542A ASN 3.2 23.8 - - - +
543A ALA* 4.1 1.6 - - - -
544A PHE* 3.9 6.7 - - + -
553A VAL* 3.4 13.2 - - + +
554A PHE* 1.3 91.7 - - - +
556A ALA* 1.3 67.3 + - - +
557A GLY 2.9 1.2 + - - -
558A ILE* 3.0 17.5 + - - +
559A LEU* 3.5 2.6 - - - +
----------------------------------------------------------
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