Contacts of the strand formed by residues 586 - 594 (chain A) in PDB entry 5FFG
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 ASN 586 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A PHE* 3.5 20.5 - - + -
560A MET 3.1 16.4 - - - +
561A GLU* 4.4 2.0 - - + -
562A TYR* 3.7 5.8 - - - -
584A PRO* 3.0 19.0 + - - +
585A ALA* 1.3 79.5 - - - +
587A ILE* 1.3 73.0 + - - +
2027A NAG 1.4 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA* 3.6 28.3 - - + +
447A GLY 3.4 36.8 - - - +
448A LEU* 3.6 11.2 - - + -
558A ILE 3.9 0.3 - - - +
559A PHE* 4.0 1.7 - - - -
560A MET* 2.9 56.0 + - + +
562A TYR* 5.2 1.6 - - + +
586A ASN* 1.3 83.5 - - - +
588A SER* 1.3 67.9 + - - +
589A ARG* 5.4 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.1 1.8 - - - -
503A LEU* 5.9 1.0 - - - +
557A THR* 3.6 22.4 - - - +
558A ILE 3.2 5.1 + - - -
559A PHE* 3.4 20.6 - - - -
586A ASN* 5.7 0.2 + - - -
587A ILE* 1.3 79.5 + - - +
589A ARG* 1.3 75.6 + - - +
2027A NAG 4.5 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 5.6 1.0 + - - -
447A GLY* 5.0 2.0 - - - -
448A LEU* 2.8 54.6 + - + +
450A VAL* 3.9 25.8 - - + +
557A THR* 4.0 2.2 - - - -
558A ILE* 2.4 46.0 + - - +
587A ILE* 5.4 6.9 - - - +
588A SER* 1.3 81.9 + - - +
590A GLN* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A VAL* 5.0 2.4 - - - +
453A SER* 4.6 9.0 - - - +
555A PRO* 3.3 31.7 - - + +
556A ILE 3.2 5.8 - - - +
557A THR* 3.5 19.7 + - - +
558A ILE* 4.6 1.6 - - - -
589A ARG* 1.3 82.0 - - - +
591A ALA* 1.3 61.1 - - - +
592A HIS* 3.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A VAL* 3.8 22.9 - - + -
453A SER 3.2 14.6 - - - +
455A LEU* 3.8 23.1 - - + -
474A PHE* 5.3 1.3 - - + -
555A PRO* 3.5 3.8 - - - +
556A ILE* 2.7 40.6 + - + +
558A ILE* 4.4 4.3 - - + -
590A GLN* 1.3 74.3 - - - +
592A HIS* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A SER* 2.8 14.8 + - - +
454A ILE* 3.3 18.5 - - + -
455A LEU* 2.5 37.5 + - - +
553A LEU 5.3 3.4 + - - -
554A THR 5.7 0.4 - - - -
555A PRO* 3.5 35.0 - - + +
590A GLN* 3.8 29.0 + - - +
591A ALA* 1.3 78.4 - - - +
593A ILE* 1.3 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU* 3.2 13.5 - - + +
457A GLN* 3.5 34.5 - - + +
511A ARG* 4.4 5.8 - - - +
543A LEU* 4.6 11.2 - - + -
549A PHE* 4.1 28.5 - - + -
552A LYS* 3.5 34.0 + - + +
553A LEU* 5.9 1.4 - - - +
554A THR 5.3 2.0 + - - +
556A ILE* 4.0 29.2 - - + -
592A HIS* 1.3 82.7 - - - +
594A LEU* 1.3 69.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 3.9 27.4 - - + +
455A LEU 3.0 37.6 + - - +
456A ASN* 3.9 23.0 - - + +
457A GLN* 3.5 26.6 + - - +
552A LYS* 4.3 14.2 + - - -
593A ILE* 1.3 81.6 - - - +
----------------------------------------------------------
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