Contacts of the strand formed by residues 503 - 511 (chain C) in PDB entry 6VVT
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 ILE 503 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 5.3 10.8 - - + -
367C ARG 5.5 1.0 + - - -
368C ARG 4.6 0.4 + - - -
369C LEU* 4.3 15.7 - - + -
446C LEU* 5.1 9.2 - - + -
473C ARG* 4.0 31.2 - - + -
474C MET* 6.0 1.3 - - + -
491C LEU* 3.7 22.9 - - + -
495C ALA* 4.1 14.1 - - + -
496C ARG 3.7 8.1 - - - +
497C VAL* 4.3 12.6 - - + +
501C GLY 3.1 8.5 + - - +
502C PHE* 1.3 73.6 - - - +
504C GLU* 1.3 71.7 + - - +
505C THR* 4.9 1.1 + - - +
523C THR* 3.7 19.2 + - - -
524C ALA* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C ALA* 3.8 1.4 - - - -
496C ARG* 2.4 61.0 + - - +
498C ASN* 3.2 27.8 - - - +
502C PHE 3.4 0.8 + - - -
503C ILE* 1.3 79.8 - - - +
505C THR* 1.3 65.4 + - - +
521C TYR* 3.9 12.8 - - + -
522C LEU 4.3 9.2 - - - +
523C THR* 4.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C TYR* 4.0 4.7 + - + -
472C GLY* 3.5 36.8 + - - +
473C ARG* 4.2 6.8 + - - +
496C ARG* 4.8 3.6 - - - -
503C ILE* 4.9 0.9 + - - +
504C GLU* 1.3 78.0 + - - +
506C PRO* 1.3 72.3 - - + +
507C TYR* 3.1 40.4 + - + +
520C ASP 3.6 1.6 - - - +
521C TYR* 4.1 0.7 - - - -
522C LEU 3.6 17.7 + - - -
527C GLU* 4.8 1.2 + - - -
576C GLN* 3.0 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.1 17.9 - - + -
494C TYR* 3.3 47.3 - - + +
496C ARG* 4.8 9.4 - - + +
504C GLU 4.4 0.2 - - - +
505C THR* 1.3 90.6 - - + +
507C TYR* 1.3 66.2 + - - +
519C ILE* 5.4 3.6 - - + -
520C ASP 4.1 4.3 - - - +
572C VAL* 3.0 27.2 - - + +
576C GLN* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C TYR* 4.1 5.6 + + - -
505C THR* 3.1 45.2 - - + +
506C PRO* 1.3 77.3 - - - +
508C ARG* 1.3 59.5 + - - +
509C LYS 3.9 1.3 + - - -
518C GLN 3.7 0.5 - - - +
519C ILE* 3.0 4.3 - - - +
520C ASP* 2.7 42.6 + - + +
522C LEU* 3.3 43.3 - - + -
527C GLU* 2.1 40.6 + - + -
532C VAL* 3.7 21.5 - - + -
553C ARG* 3.1 9.3 + - - -
569C TYR* 4.4 7.2 - - + -
570C MET 3.8 7.0 - - - +
571C ASP* 3.3 25.8 - - - -
572C VAL* 3.5 4.8 - - - +
576C GLN* 4.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 5.5 5.3 - - - +
38C PRO* 3.1 40.7 - - - +
507C TYR* 1.3 69.9 - - - +
509C LYS* 1.3 60.9 + - - +
515C VAL* 3.4 27.7 - - - +
516C THR 3.3 19.3 + - - +
517C ASP* 4.3 17.4 + - - +
518C GLN 3.4 9.4 - - - +
519C ILE* 4.3 3.6 - - + +
569C TYR* 4.3 0.4 - - - -
570C MET* 2.5 80.3 + - - +
571C ASP 3.2 14.8 + - - +
572C VAL* 3.9 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C TYR 3.9 3.0 + - - -
508C ARG* 1.3 71.3 - - - +
510C VAL* 1.3 59.5 + - - +
511C GLU* 3.9 2.8 + - + +
516C THR* 2.9 32.6 + - - -
518C GLN* 3.5 12.3 + - + +
520C ASP* 6.1 3.6 - - + +
568C ASP 3.5 9.9 - - - +
569C TYR* 3.6 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C ARG 3.3 1.4 + - - -
509C LYS* 1.3 71.2 - - - +
511C GLU* 1.3 62.5 + - - +
512C ASN 4.3 0.4 + - - -
513C GLY* 5.1 4.5 - - - +
514C VAL 3.9 12.8 - - - +
515C VAL* 4.9 4.3 - - - -
516C THR 4.6 1.1 - - - +
533C ALA* 5.4 4.0 - - + -
568C ASP* 2.6 39.9 + - - +
569C TYR 4.2 2.7 - - - -
570C MET* 4.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LYS* 3.9 4.8 + - + +
510C VAL* 1.3 74.5 - - - +
512C ASN* 1.3 103.0 + - + +
513C GLY 3.2 1.6 - - - -
514C VAL* 3.2 22.6 + - - +
516C THR* 5.2 5.8 - - - -
568C ASP 5.7 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