Contacts of the strand formed by residues 571 - 577 (chain C) in PDB entry 5NC5
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 VAL 571 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C TYR* 3.4 35.9 - - + +
328C ASP 4.0 24.5 - - - +
329C THR* 4.8 7.4 - - + -
569C GLN* 3.9 15.7 + - + +
570C GLY* 1.3 83.5 + - - +
572C PHE* 1.3 68.1 + - - +
629C VAL 3.1 10.8 - - - +
630C SER* 4.3 9.0 - - - +
631C LEU* 4.6 2.9 - - - +
644C VAL* 4.3 5.3 - - - +
667C ASN* 4.0 12.1 - - - +
668C LEU* 4.0 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 572 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C TYR* 3.9 3.9 - - - -
571C VAL* 1.3 79.2 - - - +
573C MET* 1.3 83.9 + - - +
574C THR* 3.9 0.4 - - - -
598C TYR* 3.7 34.5 - + - -
606C VAL* 5.1 0.2 - - + -
629C VAL* 2.9 60.2 + - + +
631C LEU* 3.7 30.7 - - + -
644C VAL* 4.1 20.0 - - + -
647C ILE* 3.9 20.0 - - + -
648C THR* 4.0 12.8 - - + -
665C ALA* 4.0 5.8 - - + -
666C PHE 3.4 17.5 - - - +
667C ASN* 4.3 1.8 - - - -
668C LEU* 4.6 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C SER* 6.2 4.3 - - - -
136C PHE* 5.8 0.7 - - - -
327C TYR* 3.6 21.1 - - + +
572C PHE* 1.3 79.5 - - - +
574C THR* 1.3 64.7 + - - +
617C PHE* 4.3 15.0 - - + -
626C ILE* 3.9 16.4 - - + -
627C ALA 3.6 6.5 - - - +
628C PHE* 3.6 37.5 - - + -
629C VAL 4.8 0.2 - - - +
665C ALA* 3.3 2.8 - - - -
666C PHE* 3.1 51.0 + - + +
668C LEU* 3.8 13.9 - - + -
676C THR* 4.0 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C PHE* 3.9 3.6 - - - -
573C MET* 1.3 80.3 + - - +
575C MET* 1.3 62.1 - - - +
576C VAL* 4.5 2.2 - - + +
594C VAL* 4.2 7.2 - - + -
598C TYR* 2.6 34.3 + - - +
626C ILE* 3.5 6.4 - - - +
627C ALA* 2.8 46.5 + - - +
629C VAL* 4.1 0.9 - - - +
655C PHE* 3.9 14.1 - - + -
663C VAL* 3.9 12.1 - - + -
664C PHE 3.4 21.3 - - - +
665C ALA* 3.6 2.0 - - - +
666C PHE* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C THR* 1.3 71.8 - - - +
576C VAL* 1.3 65.2 + - - +
577C GLN* 4.1 17.7 - - + +
618C ALA* 5.5 4.9 - - + -
625C GLY 4.0 4.7 - - - +
626C ILE* 4.8 4.5 - - + +
662C MET* 3.9 29.6 - - + +
663C VAL* 3.3 21.5 - - - +
664C PHE* 3.0 30.2 + - + +
666C PHE* 4.2 21.9 - - + -
717C ARG* 3.9 24.7 - - - +
718C PRO 4.4 9.6 - - - +
719C ASN* 4.7 11.7 - - - +
720C GLY 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C THR* 4.5 6.3 - - + +
575C MET* 1.3 81.5 - - - +
577C GLN* 1.3 60.8 + - - +
578C LEU* 3.5 22.2 - - + -
587C THR* 4.6 7.9 - - + -
590C VAL* 3.8 20.6 - - + -
591C LEU* 4.3 18.6 - - + -
594C VAL* 4.2 18.2 - - + -
624C THR* 3.3 7.3 + - - -
625C GLY* 2.8 43.8 + - - +
627C ALA 5.4 0.4 - - - +
662C MET 3.6 2.0 - - - -
663C VAL* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C MET* 4.1 12.4 - - + +
576C VAL* 1.3 72.7 - - - +
578C LEU* 1.3 67.9 + - - +
617C PHE 4.5 0.9 - - - +
618C ALA* 4.3 15.1 - - - +
623C ASN* 3.2 43.4 + - - +
624C THR* 3.5 18.4 + - - -
662C MET* 2.9 64.3 + - + +
720C GLY 4.5 6.7 - - - +
721C LEU* 3.4 29.6 - - + +
----------------------------------------------------------
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