Contacts of the helix formed by residues 594 - 603 (chain T) in PDB entry 2P8Z
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 ASP 594 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592T PRO 4.0 1.6 + - - -
593T ILE* 1.3 77.2 - - - +
595T GLU* 1.3 79.6 + - - +
596T GLU* 3.2 21.1 + - - +
597T VAL* 2.9 29.1 + - + +
598T SER* 3.0 11.3 + - - -
623T TYR 6.1 0.2 - - - +
625T TRP* 6.0 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 595 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593T ILE 3.5 2.6 + - - -
594T ASP* 1.3 75.7 + - - +
596T GLU* 1.3 54.7 + - - +
598T SER* 3.1 4.7 + - - -
599T LEU* 2.7 70.2 + - + +
682T ARG* 2.5 36.6 + - - -
683T SER* 4.1 4.6 + - - +
801T TRP 4.6 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 596 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594T ASP* 3.2 14.0 + - - +
595T GLU* 1.3 78.8 - - - +
597T VAL* 1.3 57.7 + - + +
599T LEU* 3.7 12.1 - - + +
600T ALA* 3.0 24.4 + - - +
623T TYR* 3.6 30.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593T ILE* 3.6 18.8 - - + -
594T ASP* 2.9 23.3 + - + +
596T GLU* 1.3 77.3 - - + +
598T SER* 1.3 65.8 + - - +
600T ALA* 3.1 6.9 + - - +
601T ILE* 2.9 34.7 + - + +
606T ILE* 4.0 13.2 - - + -
619T MET* 5.6 1.8 - - - -
623T TYR* 3.6 36.1 - - + +
625T TRP* 4.2 23.1 - - + +
645T LEU* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 598 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593T ILE* 3.7 5.3 - - - +
594T ASP 3.0 13.4 + - - -
595T GLU* 3.6 8.5 - - - -
597T VAL* 1.3 75.1 - - - +
599T LEU* 1.3 59.0 + - - +
601T ILE* 3.1 8.1 + - - +
602T GLU* 2.8 34.7 + - - +
643T PRO* 4.0 16.5 + - - +
682T ARG* 3.7 15.0 - - - -
683T SER* 2.7 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595T GLU* 2.7 43.4 + - + +
596T GLU* 3.7 12.8 - - + +
598T SER* 1.3 78.1 - - - +
600T ALA* 1.3 56.9 + - - +
602T GLU* 3.3 20.2 - - - +
603T ASN* 2.8 49.5 + - - +
682T ARG* 3.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596T GLU* 3.0 21.5 + - - +
597T VAL 3.1 7.2 + - - +
599T LEU* 1.3 76.6 - - - +
601T ILE* 1.3 60.4 + - - +
603T ASN 3.9 0.2 - - - -
604T GLY 3.2 3.6 + - - -
605T ILE* 2.8 43.1 + - + -
606T ILE* 3.2 23.0 + - + -
623T TYR* 3.7 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 601 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593T ILE* 5.2 1.8 - - + -
597T VAL* 2.9 35.1 + - + +
598T SER* 3.4 7.2 - - - +
600T ALA* 1.3 76.4 - - - +
602T GLU* 1.3 68.5 + - - +
603T ASN 3.3 0.5 + - - -
604T GLY* 3.4 6.6 + - - -
606T ILE* 3.4 35.7 - - + +
607T ASN* 4.8 1.7 - - - +
608T PRO* 5.5 3.4 - - + +
636T PHE* 4.0 21.8 - - + -
641T ASN 3.7 22.5 - - - +
642T GLY 3.8 10.1 - - - +
643T PRO* 4.0 22.0 - - + -
645T LEU* 4.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 602 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598T SER 2.8 14.8 + - - +
599T LEU* 3.3 18.3 - - - +
601T ILE* 1.3 79.3 - - - +
603T ASN* 1.3 65.9 + - - +
604T GLY 3.8 0.5 + - - -
641T ASN 5.9 0.7 - - - -
643T PRO* 3.5 24.4 - - + +
682T ARG* 2.5 48.4 + - - -
801T TRP* 4.6 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 603 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599T LEU* 2.8 48.1 + - - +
602T GLU* 1.3 82.8 + - - +
604T GLY* 1.3 57.5 + - - +
605T ILE* 3.7 15.2 - - + +
----------------------------------------------------------
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