Contacts of the strand formed by residues 624 - 628 (chain A) in PDB entry 5FWP
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 LYS 624 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LYS 3.4 25.6 + - - +
575A VAL* 4.0 2.6 - - + +
576A GLU* 2.7 38.2 + - + +
591A ILE* 3.9 12.3 - - + -
592A VAL 3.2 14.4 - - - +
593A THR* 4.5 0.9 - - - +
594A SER* 4.7 0.6 - - - +
622A ALA* 5.4 6.4 + - - +
623A LYS* 1.3 76.6 - - - +
625A HIS* 1.3 67.5 + - - +
659A PHE* 4.6 3.1 - - - -
663A LEU* 3.8 20.2 - - - -
668A PHE* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLU* 3.2 40.3 + - + +
575A VAL* 3.5 10.3 - - - -
576A GLU* 3.5 26.6 + - + +
577A LYS* 3.4 38.2 + - + +
579A THR* 5.6 4.9 - - + -
591A ILE* 3.2 8.0 - - - +
592A VAL* 2.7 44.5 + - + -
594A SER* 3.8 19.1 - - - -
624A LYS* 1.3 76.2 - - - +
626A LEU* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A MET* 3.8 24.5 - - + -
571A LEU* 3.5 30.3 - - + -
575A VAL* 3.3 15.4 - - + +
577A LYS 2.9 9.7 + - - +
578A VAL* 3.4 12.0 - - + -
579A THR* 2.8 29.6 + - - +
589A CYS* 3.8 13.7 - - + -
590A CYS 3.6 13.9 - - - +
591A ILE* 3.5 20.4 - - + +
625A HIS* 1.3 74.0 - - - +
627A GLU* 1.3 77.6 + - - +
659A PHE* 4.6 5.2 - - + -
662A ALA* 4.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLU* 4.3 5.4 - - - +
540A GLY 4.6 1.7 + - - -
579A THR* 3.2 19.9 - - + +
581A SER* 2.8 28.1 + - - -
583A ARG* 2.6 50.9 + - - +
584A LEU* 4.0 8.6 - - + +
589A CYS* 3.0 9.0 - - - +
590A CYS 2.8 34.2 + - - +
592A VAL* 3.6 23.5 - - + +
626A LEU* 1.3 76.6 - - - +
628A ILE* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A PHE* 5.5 1.1 - - + -
563A LEU* 5.1 3.4 - - + -
564A CYS* 3.4 31.4 - - - +
567A MET* 3.5 28.7 - - + -
578A VAL* 3.4 23.3 - - + -
579A THR 2.6 13.8 + - - +
580A ILE* 3.5 11.2 - - + +
581A SER 3.0 23.4 + - - +
584A LEU* 4.1 3.1 - - - -
588A PRO 3.7 3.6 - - - +
589A CYS* 4.9 0.4 - - + -
626A LEU* 4.9 1.3 - - + -
627A GLU* 1.3 79.1 - - - +
629A ASN* 1.3 65.0 + - - +
630A PRO* 3.0 9.8 - - + +
635A VAL* 3.5 34.1 - - + -
----------------------------------------------------------
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