Contacts of the strand formed by residues 669 - 674 (chain q) in PDB entry 6FF7
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 ARG 669 (chain q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604q HIS* 5.1 15.9 - - + +
609q PRO* 6.5 0.4 - - + -
610q GLY 4.3 17.9 - - - +
612q ILE* 6.5 0.4 - - + -
642q GLU 2.9 5.7 + - - +
643q LEU* 3.3 9.7 - - + -
644q LEU* 2.9 25.8 + - - +
664q THR* 3.9 9.8 - - - -
665q PRO 5.2 0.3 - - - -
667q GLY 4.7 2.9 - - - +
668q ALA* 1.3 77.3 - - - +
670q LYS* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 670 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611q ASP* 3.5 17.9 - - + +
612q ILE* 2.9 26.0 + - - +
643q LEU* 6.2 0.2 - - - -
644q LEU* 3.6 11.7 - - + +
660q ILE 5.9 2.7 - - - +
662q GLN 4.9 7.9 - - - +
663q PRO 5.5 0.2 - - - -
664q THR* 3.8 21.4 - - - +
669q ARG* 1.3 79.5 - - - +
671q VAL* 1.3 63.3 + - - +
672q VAL 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 671 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600q VAL* 5.9 6.7 - - + -
612q ILE* 3.4 15.3 - - + +
614q VAL* 6.4 1.8 - - + -
629q LEU* 6.1 3.8 - - + -
643q LEU* 6.2 2.2 - - + -
644q LEU 2.8 14.0 + - - +
645q VAL* 3.3 9.1 - - + +
646q LEU* 2.9 26.7 + - - +
670q LYS* 1.3 78.0 - - - +
672q VAL* 1.3 62.3 + - - +
673q VAL* 4.0 0.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 672 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612q ILE 2.9 11.3 + - - +
613q LEU* 3.5 7.2 - - + +
614q VAL* 2.9 27.2 + - - +
646q LEU* 3.5 8.7 - - + +
648q ILE* 6.0 3.8 - - + -
660q ILE* 5.1 17.5 - - + +
670q LYS 4.1 0.2 - - - -
671q VAL* 1.3 74.8 - - - +
673q VAL* 1.3 61.9 + - - +
674q ALA* 3.7 6.9 + - + +
684q ILE* 5.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 673 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614q VAL* 3.4 15.0 - - + +
616q LEU* 5.4 4.9 - - + -
622q ILE* 4.8 22.7 - - + +
625q ALA* 5.1 10.3 - - + -
626q CYS* 5.6 4.9 - - + +
646q LEU 2.8 14.3 + - - +
647q PRO* 3.6 5.1 - - + +
648q ILE 2.8 27.1 + - - +
671q VAL* 4.0 1.6 + - + -
672q VAL* 1.3 70.9 - - - +
674q ALA* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 674 (chain q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613q LEU* 6.2 2.0 - - + -
614q VAL 2.7 13.8 + - - +
615q PHE* 3.1 6.9 - - - -
616q LEU* 2.6 35.3 + - - +
622q ILE* 6.2 1.6 - - - -
648q ILE* 3.5 15.9 - - + +
672q VAL* 3.7 8.0 + - + +
673q VAL* 1.3 75.6 - - - +
675q THR* 1.3 66.9 + - - +
677q ILE* 5.8 1.1 - - + -
678q ALA* 3.7 22.2 - - + +
----------------------------------------------------------
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