Contacts of the helix formed by residues 587 - 596 (chain D) in PDB entry 5IWM
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 587 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 5.9 0.8 + - - -
106A GLY 4.2 5.2 + - - +
107A GLN* 3.6 17.0 - - - +
108A GLY* 2.8 32.0 + - - +
585D GLU 4.2 0.2 + - - -
586D MET* 1.3 74.5 - - - +
588D ALA* 1.3 68.3 + - - +
589D ASP* 3.1 18.8 + - - +
590D GLN* 3.0 40.5 + - - +
591D LEU* 3.2 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 588 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY 5.6 0.6 + - - -
298A LEU* 3.7 22.9 - - + -
442D SER* 3.8 15.7 + - - +
445D SER* 3.7 27.4 - - - -
446D GLY* 3.8 7.8 - - - +
586D MET 3.7 2.0 + - - -
587D ASN* 1.3 71.6 - - - +
589D ASP* 1.3 61.4 + - - +
591D LEU* 3.3 5.5 + - - +
592D TRP* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 589 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.7 15.8 - - + +
299A ARG* 5.8 0.7 - - - +
587D ASN* 3.2 21.7 + - - +
588D ALA* 1.3 74.0 - - - +
590D GLN* 1.3 66.1 + - - +
592D TRP* 3.2 8.5 + - + +
593D GLU* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 590 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLN* 3.9 11.6 + - - +
580D TYR* 3.7 19.4 + - - +
586D MET* 3.6 19.2 - - + +
587D ASN* 3.0 49.6 + - + +
589D ASP* 1.3 86.3 + - - +
591D LEU* 1.3 52.5 + - - +
593D GLU* 4.2 4.5 - - - +
594D THR* 2.5 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D SER* 3.6 39.3 - - - +
443D THR* 3.7 18.2 - - + +
446D GLY* 6.0 0.4 - - - -
506D MET* 4.4 7.0 - - - -
583D LEU* 4.1 25.1 - - + +
586D MET* 3.8 28.0 - - + -
587D ASN 3.2 9.2 + - - +
588D ALA* 3.6 7.9 - - - +
589D ASP 3.2 0.8 - - - -
590D GLN* 1.3 76.6 - - - +
592D TRP* 1.3 61.6 + - - +
594D THR* 3.9 0.4 - - - -
595D THR* 3.0 49.0 + - - +
596D MET* 3.3 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 592 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG* 3.2 44.4 - - + +
446D GLY* 3.2 30.3 - - - +
448D ASP* 4.4 12.1 - - + -
452D GLN* 3.9 22.4 - - - -
588D ALA 3.1 11.1 + - - +
589D ASP* 3.2 7.4 + - + +
591D LEU* 1.3 75.4 - - - +
593D GLU* 1.3 91.9 + - + +
596D MET* 3.2 16.2 + - + -
597D ASN* 2.7 74.1 + - - +
598D PRO* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 593 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ARG* 5.8 1.0 - - - -
589D ASP* 2.9 21.6 + - + +
590D GLN* 4.7 3.8 - - - +
592D TRP* 1.3 94.4 + - + +
594D THR* 1.3 65.2 + - + +
597D ASN* 3.2 13.4 + - - +
600D HIS* 2.9 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 594 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN 4.4 7.3 - - - +
543D PRO* 3.7 26.3 - - + +
586D MET* 5.5 0.2 - - + -
590D GLN* 2.5 29.4 + - + +
591D LEU* 3.8 1.4 + - - -
593D GLU* 1.3 82.5 - - + +
595D THR* 1.3 71.8 + - - +
600D HIS 4.4 2.5 - - - +
601D ARG* 4.1 13.7 - - - -
602D ALA 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 595 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D PHE* 4.8 2.4 - - - -
506D MET* 3.7 25.4 - - - -
540D ALA* 3.9 2.7 - - + -
541D GLN 3.9 14.0 + - - +
542D PRO* 3.4 39.2 - - + +
543D PRO* 3.7 2.6 - - - +
591D LEU* 3.0 20.8 + - - +
594D THR* 1.3 90.9 + - - +
596D MET* 1.3 60.3 + - - +
601D ARG* 3.3 21.6 - - - +
603D LEU* 4.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 596 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D PHE* 3.8 34.3 - - + -
443D THR* 3.8 37.9 - - + +
446D GLY 4.9 3.1 - - - -
447D ARG* 3.9 17.0 - - + -
452D GLN* 3.1 32.2 + - + +
454D ILE* 4.9 1.1 - - + -
506D MET* 4.1 12.1 - - - -
591D LEU* 3.3 21.0 + - + +
592D TRP* 3.2 19.0 + - + +
595D THR* 1.3 79.1 - - - +
597D ASN* 1.3 61.5 + - - +
598D PRO 3.2 0.9 - - - -
601D ARG* 3.0 29.0 + - - +
----------------------------------------------------------
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