Contacts of the helix formed by residues 638 - 643 (chain C) in PDB entry 4AY6
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 ASN 638 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C CYS* 3.9 19.5 - - - -
628C ASN* 3.1 28.8 + - - +
630C ASN* 5.1 0.7 - - - +
631C GLY* 3.1 31.5 + - - +
632C TYR* 3.8 21.0 - - - -
636C ALA* 4.0 6.3 - - - +
637C ARG* 1.3 73.5 + - - +
639C GLU* 1.3 69.4 + - - +
640C LEU 3.0 2.2 - - - -
641C PHE* 2.8 21.0 + - - +
642C ALA* 2.9 12.5 + - - +
663C PHE* 4.2 14.9 - - + -
1398G GLN* 4.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 639 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C CYS* 3.9 23.9 - - + +
524C LYS* 3.2 35.4 + - + +
525C ILE* 3.6 21.2 - - + +
611C ASN* 3.0 32.0 + - - +
636C ALA 5.0 0.2 - - - +
637C ARG* 3.6 9.3 - - - -
638C ASN* 1.3 83.1 + - - +
640C LEU* 1.3 60.3 + - - +
642C ALA* 3.3 8.4 + - - +
643C LEU* 3.2 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 640 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C VAL* 4.3 11.0 - - + -
583C LEU* 4.0 15.9 - - + -
605C LEU* 3.9 23.6 - - + -
611C ASN* 3.8 18.6 - - - +
614C ALA* 3.4 32.3 - - + -
615C ALA* 3.7 14.8 - - - +
618C ILE* 4.4 11.4 - - + -
626C LEU* 5.5 1.6 - - + -
637C ARG* 3.4 23.3 + - + +
638C ASN 3.0 0.8 - - - -
639C GLU* 1.3 77.4 - - - +
641C PHE* 1.3 67.1 + - + +
643C LEU* 3.3 16.3 + - - +
645C PRO* 3.5 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 641 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C VAL* 4.0 27.6 - - + -
626C LEU* 3.6 32.3 - - + -
627C VAL 3.8 5.6 - - - -
628C ASN* 3.3 59.5 - - + -
637C ARG 4.4 4.9 - - - -
638C ASN* 2.8 20.7 + - - +
640C LEU* 1.3 77.4 - - + +
642C ALA* 1.3 58.2 + - - +
644C ARG* 2.8 22.5 + - - -
645C PRO* 4.7 0.9 - - - -
649C GLN* 3.0 30.0 + - + +
663C PHE* 3.7 23.1 - - + +
664C MET* 3.8 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 642 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C CYS* 4.5 6.5 - - + -
522C LEU* 4.8 9.6 - - + +
525C ILE* 4.2 23.9 - - + +
638C ASN 2.9 11.2 + - - +
639C GLU* 3.5 15.5 - - - +
641C PHE* 1.3 75.9 - - - +
643C LEU* 1.3 60.7 + - - +
644C ARG* 3.1 6.5 + - - +
663C PHE* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 643 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C ILE* 3.8 37.7 - - + +
528C LEU* 4.8 4.0 - - + -
530C LYS* 4.2 29.4 - - + -
532C PRO* 5.8 1.6 - - - +
533C TYR* 3.4 16.6 + - + -
611C ASN 3.4 31.9 - - - +
612C GLY* 4.4 4.3 - - - +
615C ALA* 3.6 19.3 - - + -
639C GLU 3.2 18.7 + - - +
640C LEU* 3.6 7.2 - - - +
641C PHE 3.0 1.4 - - - -
642C ALA* 1.3 73.8 - - - +
644C ARG* 1.3 73.9 + - - +
645C PRO 3.7 0.7 - - - -
----------------------------------------------------------
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