Contacts of the helix formed by residues 618 - 622 (chain A) in PDB entry 4N78
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 618 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 4.2 21.3 - - - +
408A VAL* 4.2 13.9 - - + -
409A MET* 3.5 30.7 - - + -
455A ILE* 4.0 26.2 - - + -
458A ILE* 4.2 17.5 - - + -
459A LYS* 4.5 8.3 - - + -
616A CYS 3.4 12.0 + - - +
617A ASP* 1.3 79.1 + - - +
619A SER* 1.3 62.6 + - - +
620A GLN 3.2 4.0 + - - -
621A LEU* 3.7 16.8 + - + +
670A LEU* 3.7 33.0 - - + +
673A ASP* 4.2 11.7 + - - +
674A SER* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ASP* 2.7 24.3 + - - -
618A LEU* 1.3 77.5 - - - +
620A GLN* 1.3 77.1 + - - +
621A LEU 3.3 0.9 - - - -
622A TRP 4.0 0.2 + - - -
623A PHE* 3.1 15.4 - - - -
673A ASP* 3.4 36.0 - - - +
674A SER* 2.9 20.0 + - - -
677A TYR* 3.1 18.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO* 6.5 1.3 - - + -
309A GLY* 3.5 37.2 + - - +
310A ASP* 5.3 2.1 - - - +
409A MET* 4.8 13.0 - - - -
412A TYR* 3.6 18.8 + - + -
617A ASP* 4.9 6.3 + - - +
618A LEU 3.2 1.8 - - - -
619A SER* 1.3 100.8 + - - +
621A LEU* 1.3 63.4 + - - +
622A TRP 3.1 3.6 + - - -
623A PHE* 3.6 27.2 + - - +
677A TYR* 3.5 33.6 - - - -
682A PHE* 4.2 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 4.5 5.2 - - + -
409A MET* 3.5 29.4 - - + -
412A TYR* 3.5 49.3 + - + -
435A TYR* 4.7 4.0 + - - -
455A ILE* 4.3 12.6 - - + -
618A LEU* 3.9 7.4 - - + +
619A SER 3.3 1.6 - - - -
620A GLN* 1.3 79.1 - - - +
622A TRP* 1.3 58.7 + - - +
623A PHE 4.7 0.2 - - - +
644A MET* 3.6 36.8 + - + +
645A PRO* 4.1 6.7 - - + +
648A LEU* 4.8 7.6 - - + -
670A LEU* 4.0 35.0 - - + -
674A SER* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A SER 4.0 1.2 + - - -
620A GLN 3.1 0.6 - - - -
621A LEU* 1.3 80.8 - - - +
623A PHE* 1.3 92.5 + + - +
624A ARG* 3.2 37.8 + - + +
625A GLU* 5.6 0.9 - - - -
637A GLN* 4.0 19.5 - - - -
643A SER* 3.5 19.1 - - - -
645A PRO* 4.0 12.1 - - + -
671A TYR* 3.9 16.4 - + + -
674A SER* 3.3 23.3 + - - +
687A LEU* 3.8 18.6 - - + -
690A GLU* 4.0 9.0 - - + -
691A ILE* 3.4 47.6 - - + -
694A GLU* 2.6 33.1 + - - +
----------------------------------------------------------
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