Contacts of the strand formed by residues 583 - 591 (chain I) in PDB entry 5G04
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 LEU 583 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577I ASN* 2.5 26.0 + - - +
578I ASN 2.9 16.7 + - - -
581I SER* 3.2 28.4 - - - +
582I ASN* 1.3 84.4 - - - +
584I HIS* 1.3 61.0 + - - +
585I TYR* 3.5 32.9 + - + +
602I ARG* 4.0 15.3 - - + +
603I ARG 3.5 7.6 - - - +
604I HIS* 3.5 37.2 - - + +
605I THR 4.2 1.3 - - - +
611I VAL* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 584 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I CYS* 2.4 48.2 - - - +
211I SER* 2.8 36.3 + - - -
216I SER* 4.0 7.4 + - - -
218I SER* 2.4 30.1 + - - +
233I TYR* 4.6 9.9 - - - +
235I GLN* 5.1 2.5 - - - +
575I LEU* 5.1 2.2 - - + -
576I TRP 3.6 2.5 - - - -
577I ASN* 3.7 13.3 - - - -
583I LEU* 1.3 71.3 - - - +
585I TYR* 1.3 62.3 + - - +
601I LEU* 5.4 0.8 - - - +
602I ARG* 3.0 8.5 - - - +
603I ARG* 2.9 38.8 + - + +
604I HIS 5.6 0.2 - - - +
605I THR* 4.1 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 585 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574I PHE 3.8 0.7 - - - +
575I LEU* 3.4 8.1 - - - +
576I TRP* 2.5 45.9 + + - +
578I ASN* 4.3 19.1 - - + -
581I SER* 4.4 2.4 + - - -
583I LEU* 3.5 29.4 - - + +
584I HIS* 1.3 75.1 - - - +
586I LEU* 1.3 60.1 + - - +
587I LEU 4.2 0.2 - - - -
600I ILE* 3.8 16.2 - - + -
601I LEU 3.4 0.9 - - - -
602I ARG* 2.7 58.5 + - + -
643I PHE* 3.4 40.1 - + + -
646I ASP 5.3 0.7 - - - -
671I LEU* 4.6 8.7 - - + +
675I TYR* 3.7 17.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220I VAL* 4.2 8.7 - - + -
233I TYR* 3.6 28.3 - - + -
556I LEU* 3.7 30.5 - - + -
573I PRO* 3.7 17.0 - - + -
574I PHE 3.5 14.4 - - - +
575I LEU* 3.9 15.3 - - + -
584I HIS 4.2 0.2 - - - -
585I TYR* 1.3 74.1 - - - +
587I LEU* 1.3 82.3 + - - +
588I PHE* 4.0 9.6 - - + -
599I CYS 3.8 0.5 - - - +
600I ILE* 3.6 3.3 - - - -
601I LEU* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572I PHE* 3.6 14.8 - - + -
573I PRO* 3.2 9.2 - - - +
574I PHE* 2.9 36.7 + - + +
586I LEU* 1.3 75.7 - - - +
588I PHE* 1.3 62.0 + - - +
598I MET* 4.3 5.6 - - + -
599I CYS 3.5 3.1 - - - +
600I ILE* 3.7 31.9 - - + -
641I ALA* 4.0 22.7 - - + +
642I GLN* 4.1 3.1 - - - +
643I PHE* 3.5 36.6 - - + +
649I VAL* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 588 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556I LEU* 4.0 17.3 - - + -
557I TYR* 4.1 15.3 - + + -
572I PHE* 3.7 8.8 - - - -
573I PRO* 4.1 17.9 - - + -
586I LEU* 4.0 13.0 - - + -
587I LEU* 1.3 77.9 - - - +
589I THR* 1.3 65.3 + - - +
590I ILE* 3.8 28.3 - - + -
598I MET* 3.8 0.9 - - - +
599I CYS* 2.8 64.8 + - + +
601I LEU* 4.0 13.2 - - + -
615I LEU* 3.8 13.2 - - + -
693I LEU* 3.6 33.0 - - + -
700I ILE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 589 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557I TYR* 3.9 8.1 + - - -
561I ARG* 2.5 53.9 + - - +
572I PHE* 3.5 25.8 - - + -
588I PHE* 1.3 79.7 - - - +
590I ILE* 1.4 59.9 + - - +
596I TYR* 3.8 19.6 - - - -
597I LYS 3.2 9.6 - - - +
598I MET* 4.1 3.6 - - + -
638I CYS* 3.7 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 590 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556I LEU 4.7 1.8 - - - +
557I TYR* 4.2 17.5 - - + -
561I ARG* 3.7 3.4 - - - +
588I PHE* 3.8 26.7 - - + -
589I THR* 1.4 79.8 - - - +
591I LEU* 1.3 61.9 + - - +
592I GLU* 3.8 3.5 + - + +
596I TYR* 4.4 0.9 - - - -
597I LYS* 2.9 40.9 + - + +
599I CYS* 3.7 23.8 - - - -
693I LEU 5.4 0.9 - - - -
694I ASP* 4.6 18.4 - - + -
697I CYS* 4.7 18.2 - - + -
700I ILE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559I ASP* 3.6 33.7 - - + +
561I ARG* 4.0 6.8 - - + +
590I ILE* 1.3 74.0 - - - +
592I GLU* 1.3 59.8 + - - +
594I SER* 4.3 19.3 - - - +
595I LEU 3.8 8.5 - - - +
596I TYR* 3.4 41.3 - - + +
697I CYS* 5.7 1.3 - - - -
----------------------------------------------------------
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