Contacts of the helix formed by residues 516 - 525 (chain C) in PDB entry 2W4V
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 LEU 516 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C GLU* 3.4 17.5 - - + +
485C GLN* 5.3 7.9 - - + -
486C GLN* 4.2 13.5 - - + +
489C ASN* 5.3 4.9 + - - +
515C ASP* 1.3 80.5 - - - +
517C GLN* 1.3 66.3 + - - +
518C MET* 2.5 10.8 + - + +
519C CYS* 2.8 42.1 + - + -
520C ILE* 2.6 26.3 + - + +
561C MET* 4.1 13.0 - - + -
581C HIS 5.0 2.7 - - - +
583C TYR* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C GLN* 4.3 12.2 - - - +
515C ASP* 2.7 21.8 + - - +
516C LEU* 1.3 76.7 - - - +
518C MET* 1.3 57.8 + - + +
520C ILE* 2.9 16.2 - - + +
521C ASP* 2.4 57.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 518 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C ASP* 4.5 12.6 - - - +
516C LEU* 2.5 7.0 + - + +
517C GLN* 1.3 75.4 + - + +
519C CYS* 1.3 61.6 + - - +
520C ILE 2.8 0.7 - - - -
521C ASP* 2.1 37.8 + - - -
522C LEU* 2.5 16.2 + - + -
559C ASN* 5.5 8.3 - - + +
560C ARG* 6.2 3.4 - - - +
561C MET* 4.4 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 519 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C GLU* 3.2 24.5 - - + +
516C LEU* 2.8 56.4 + - + -
518C MET* 1.3 82.6 - - - +
520C ILE* 1.3 73.2 + - - +
522C LEU* 3.2 16.4 + - - +
523C ILE* 3.0 17.8 + - - +
561C MET* 3.3 27.6 - - + +
580C LEU* 5.8 4.9 - - + +
581C HIS 4.4 5.2 - - - +
582C HIS* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C TYR* 3.4 15.4 - - + +
482C GLU* 4.4 11.4 - - + -
483C ARG* 4.4 19.7 - - + -
486C GLN* 4.1 16.8 - - + -
516C LEU* 2.6 38.8 - - + +
517C GLN* 2.9 20.4 - - + +
518C MET 2.5 2.4 + - - -
519C CYS* 1.3 95.4 - - - +
521C ASP* 1.3 52.7 + - - +
523C ILE* 2.4 32.2 - - - +
524C GLU* 2.7 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C GLN* 2.4 47.2 + - - +
518C MET* 2.1 25.8 + - - +
520C ILE* 1.3 63.6 - - - +
522C LEU* 1.3 67.1 + - + +
523C ILE 3.1 2.2 - - - -
524C GLU* 5.1 0.2 - - - -
525C LYS* 2.7 62.8 + - - +
528C GLY* 4.2 3.1 - - - -
555C HIS* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 522 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C MET* 2.5 14.7 + - + +
519C CYS* 3.4 11.2 - - - +
521C ASP* 1.3 75.3 + - - +
523C ILE* 1.3 50.2 + - - +
528C GLY* 3.2 5.4 - - - -
529C ILE* 2.6 39.1 + - + +
555C HIS* 3.1 40.9 + - + +
559C ASN* 3.4 20.4 - - + +
561C MET* 2.8 45.3 - - + +
562C PHE* 3.7 17.0 - - + +
580C LEU* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C LEU* 5.8 5.8 - - + +
479C TYR* 2.3 67.5 - - + -
519C CYS 3.0 13.0 - - - +
520C ILE* 2.4 26.9 - - - +
522C LEU* 1.3 81.5 - - - +
524C GLU* 1.3 57.7 + - - +
528C GLY* 4.0 1.1 - - - -
529C ILE* 2.5 56.0 + - + -
530C LEU* 3.3 35.1 + - + +
531C SER 4.4 0.2 + - - -
580C LEU* 5.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C TYR* 2.3 33.4 - - + +
520C ILE* 2.7 19.3 + - + +
523C ILE* 1.3 73.9 - - - +
525C LYS* 1.3 71.6 + - - +
526C PRO 4.6 0.7 - - - -
530C LEU* 5.3 3.1 - - + +
531C SER* 4.9 3.8 + - - -
650C ARG* 3.1 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 525 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C ASP* 2.7 55.8 + - - +
524C GLU* 1.3 88.4 - - - +
526C PRO* 1.4 110.3 - - + +
527C MET* 3.3 3.1 - - - +
528C GLY* 2.5 30.5 + - - +
531C SER* 3.7 2.3 + - - -
----------------------------------------------------------
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