Contacts of the strand formed by residues 574 - 579 (chain E) in PDB entry 3NVQ
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 THR 574 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572E HIS 5.1 0.3 + - - -
573E ALA* 1.3 73.3 - - - +
575E TYR* 1.3 62.8 + - - +
576E SER* 4.2 6.4 + - - +
586E SER* 4.3 12.8 - - - +
587E CYS 3.5 11.7 - - - +
588E GLU* 4.1 17.1 + - - +
589E PRO* 3.5 18.2 - - - +
614E GLU 3.4 1.6 - - - +
615E ALA* 3.3 3.5 - - - -
616E GLN* 2.8 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 575 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566E CYS* 3.9 22.0 - - - -
567E PRO 4.4 5.2 - - - -
568E MET* 3.4 42.2 - - + -
569E GLU* 3.1 21.9 + - - +
570E SER* 3.1 30.1 + - - -
573E ALA* 3.7 16.4 - - + -
574E THR* 1.3 75.8 - - - +
576E SER* 1.3 62.8 + - - +
586E SER* 3.4 2.4 + - - -
587E CYS* 2.8 41.5 + - + +
596E CYS* 3.7 22.4 - - + -
613E CYS* 4.0 5.8 - - - -
614E GLU 3.2 3.4 - - - -
615E ALA* 3.6 26.0 - - + +
622E ARG* 5.2 4.4 + - - -
624E ALA* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 576 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574E THR* 4.6 6.8 + - - +
575E TYR* 1.3 74.4 - - - +
577E TRP* 1.3 62.9 + - - +
578E ARG* 3.7 23.6 + - - +
583E VAL* 4.7 11.0 - - - +
585E GLN 3.4 7.2 - - - -
586E SER* 3.4 17.3 + - - -
612E PHE 3.3 2.3 - - - +
613E CYS* 3.2 4.3 - - - -
614E GLU* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 577 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E LEU* 3.4 51.1 + - + -
565E SER 3.8 0.7 - - - -
566E CYS* 3.6 20.2 - - + +
576E SER* 1.3 71.9 - - - +
578E ARG* 1.3 59.4 + - - +
583E VAL* 3.4 4.5 - - - -
584E GLU* 2.8 28.0 + - - -
585E GLN* 2.9 16.1 + - + +
596E CYS* 2.9 37.2 + - - -
597E ILE 4.1 0.9 - - - -
598E LEU* 3.6 37.2 - - + +
611E TYR* 4.1 17.7 - - + -
612E PHE 3.1 28.7 - - - -
613E CYS* 3.7 20.0 - - + -
625E GLN* 3.8 23.3 - - + -
627E TRP* 4.1 7.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 578 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576E SER* 3.7 16.8 + - - +
577E TRP* 1.3 75.2 - - - +
579E HIS* 1.3 61.9 + - - +
581E GLU* 3.8 20.4 + - - +
582E ASN 3.4 20.2 - - - +
583E VAL* 3.8 24.6 - - - +
610E HIS 3.8 0.7 - - - +
611E TYR* 3.3 9.0 - - - -
612E PHE* 2.6 51.2 + - + +
614E GLU* 3.8 28.8 + - + +
621E PHE* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 579 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578E ARG* 1.3 74.5 - - - +
580E LYS* 1.3 89.5 + - + +
581E GLU 3.1 0.2 - - - -
582E ASN* 3.0 24.2 + - - +
584E GLU* 3.4 18.9 + - + +
606E GLN 3.4 10.5 - - - -
607E GLN* 3.4 32.5 - - - +
608E TYR 2.9 23.1 + - - -
610E HIS 3.0 27.6 - - - -
611E TYR* 3.3 34.3 + + + -
612E PHE* 6.0 0.2 - - - -
----------------------------------------------------------
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