Contacts of the strand formed by residues 594 - 599 (chain E) in PDB entry 6V3O
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 594 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591E ILE* 3.1 32.2 + - - +
592E LYS 4.1 8.1 - - - +
593E GLY* 1.3 85.5 - - - +
595E GLN* 1.3 61.1 + - - +
633E VAL* 4.1 2.2 - - - +
634E LYS* 3.3 48.9 - - + +
636E THR* 4.7 7.7 + - - -
667E SER* 5.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 595 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561E VAL 3.1 20.4 + - - -
563E PRO* 3.8 10.5 - - - +
578E VAL* 5.5 2.7 - - + -
581E LEU* 5.8 4.4 - - - +
582E PHE* 4.0 19.0 - - + -
587E TYR* 2.5 36.4 + - - -
591E ILE* 4.1 5.4 - - + +
594E LYS* 1.3 74.7 - - - +
596E GLN* 1.3 83.6 + - - +
597E VAL* 4.2 5.8 - - + +
633E VAL* 3.9 16.5 - - + +
634E LYS 3.2 10.4 + - - +
635E LEU* 3.3 14.5 - - + +
636E THR* 2.9 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 596 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531E PRO* 4.0 10.9 - - - +
560E PRO* 5.9 4.2 - - + +
562E VAL* 3.2 42.7 - - + +
595E GLN* 1.3 92.8 + - - +
597E VAL* 1.3 65.6 + - - +
636E THR* 3.2 29.5 - - + +
638E PHE* 3.5 15.4 - - + +
669E ARG* 2.9 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562E VAL* 3.7 5.2 - - - -
563E PRO* 3.7 23.1 - - + +
565E PHE* 3.8 21.8 - - + -
578E VAL* 4.5 8.3 - - + -
595E GLN* 4.2 8.1 - - + -
596E GLN* 1.3 80.8 - - - +
598E MET* 1.3 68.1 + - - +
599E VAL* 4.2 2.4 + - + -
624E MET* 3.6 36.6 - - + -
635E LEU* 4.0 12.1 - - + +
636E THR 3.0 6.5 + - - -
637E LEU* 3.4 15.1 - - + +
638E PHE* 2.9 22.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 598 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TRP* 3.6 31.4 - - + -
456E ARG* 5.1 0.4 - - - +
533E ILE* 4.1 10.1 - - + -
562E VAL* 3.6 7.5 - - + +
563E PRO 3.0 14.2 + - - +
564E LEU* 3.5 34.0 - - + +
565E PHE* 3.3 23.6 + - - +
597E VAL* 1.3 77.4 - - - +
599E VAL* 1.3 65.9 + - - +
600E GLY* 5.6 0.9 - - - -
603E ASP* 5.8 0.7 - - - +
638E PHE* 3.3 46.9 - - + +
640E GLY* 3.6 27.1 - - - -
641E ARG 5.0 0.9 - - - +
671E THR* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 599 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564E LEU* 4.1 3.6 - - - -
565E PHE* 4.3 4.9 - - + +
571E LEU* 4.5 13.7 - - + -
597E VAL* 5.0 4.9 - - + -
598E MET* 1.3 81.1 - - - +
600E GLY* 1.3 58.9 + - - +
601E TYR* 4.2 5.7 - - + +
617E LEU* 3.6 30.7 - - + -
620E ALA* 6.1 1.1 - - + -
621E GLN* 4.8 9.2 - - + +
624E MET* 5.6 6.1 - - - -
637E LEU* 4.8 18.4 - - + -
638E PHE 3.0 11.4 + - - +
639E HIS* 4.2 24.0 - - + +
640E GLY* 2.8 28.1 + - - -
----------------------------------------------------------
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