Contacts of the strand formed by residues 585 - 591 (chain C) in PDB entry 3QCA
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 PHE 585 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C ARG* 3.3 50.0 - - + +
578C ILE 3.5 3.6 - - - -
579C ARG* 3.5 33.2 - - + -
583C GLY 4.6 10.5 - - - -
584C GLU* 1.3 85.2 + - - +
586C LEU* 1.3 65.2 + - - +
587C GLU* 3.7 6.1 + - - +
643C THR* 4.5 12.3 - - + -
645C PHE* 5.3 4.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C ARG* 3.4 4.5 - - - +
578C ILE* 2.8 46.7 + - + +
580C THR* 3.9 24.2 - - + +
584C GLU 3.8 2.0 + - - -
585C PHE* 1.3 75.1 - - - +
587C GLU* 1.3 59.9 + - - +
602C PHE* 4.2 7.9 - - + -
603C VAL* 4.5 18.6 - - + -
606C LYS* 3.6 50.3 - - + +
608C PHE* 4.1 12.8 - - + -
646C LEU* 4.6 1.3 - - + -
623D ASP* 6.4 1.1 - - + -
626D GLN* 5.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C LYS* 3.5 21.7 + - + -
576C LEU 3.5 11.4 - - - +
577C ARG* 3.3 37.3 + - + -
585C PHE* 3.7 6.4 + - - +
586C LEU* 1.3 77.5 - - - +
588C ARG* 1.3 76.9 + - - +
589C ARG* 5.8 3.6 - - - -
602C PHE* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ARG* 5.0 10.5 - - - +
594A ASN* 5.2 2.0 - - - +
598A ILE* 3.4 51.4 + - + +
601A ASP* 3.9 27.8 + - - +
575C LYS* 4.9 0.4 - - - -
576C LEU 2.9 32.5 + - - +
587C GLU* 1.3 80.8 - - - +
589C ARG* 1.3 77.3 + - - +
590C PHE* 3.6 32.1 - - + -
598C ILE* 5.6 0.6 - - - +
602C PHE* 3.4 48.3 - - + +
606C LYS* 5.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571A GLU* 4.5 8.9 + - - -
591A LEU* 3.6 27.5 - - + +
593A SER* 3.5 25.9 + - - -
594A ASN* 3.6 36.1 + - - +
595A LYS* 4.8 3.4 - - - +
573C VAL* 5.2 6.7 - - + +
574C SER 3.0 7.0 - - - +
575C LYS* 3.7 37.5 - - + +
587C GLU* 5.8 3.6 - - - -
588C ARG* 1.3 88.9 + - - +
590C PHE* 1.3 69.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A LEU* 4.1 9.4 - - - +
594A ASN* 5.1 1.3 - - - -
573C VAL* 3.8 5.5 - - - -
574C SER 2.8 31.6 + - - +
576C LEU* 3.7 25.4 - - + -
588C ARG* 3.6 38.1 - - + -
589C ARG* 1.3 80.5 - - - +
591C LEU* 1.3 69.6 + - - +
592C ALA 3.3 0.2 + - - -
594C ASN* 3.9 6.7 - - + +
598C ILE* 3.4 34.5 - - + -
599C VAL* 4.1 19.5 - - + -
602C PHE* 3.8 35.9 - + + -
633C LEU* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A PRO 5.8 0.9 - - - +
573A VAL* 5.1 8.5 - - + -
589A ARG* 3.4 49.8 - - + +
590A PHE* 4.1 26.0 - - - +
591A LEU* 4.3 12.2 - - + +
571C GLU* 4.0 16.8 - - + +
572C PRO 4.1 3.1 - - - -
574C SER* 3.8 0.2 - - - -
590C PHE* 1.3 74.7 - - - +
592C ALA* 1.3 58.5 + - - +
593C SER* 2.9 17.5 - - - +
594C ASN* 2.9 54.6 + - - +
633C LEU* 3.5 8.7 - - - +
----------------------------------------------------------
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