Contacts of the strand formed by residues 144 - 148 (chain D) in PDB entry 2W3S
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 VAL 144 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLU* 3.8 20.6 - - + +
142D GLY 5.1 1.6 - - - +
143D PRO* 1.3 77.2 - - - +
145D ILE* 1.3 62.1 + - - +
146D TRP* 3.7 26.7 - - + +
309D ASP* 5.3 0.4 - - - +
312D MET* 3.6 14.3 - - - +
326D ILE 3.6 1.4 - - - +
327D GLU* 3.3 2.9 - - - -
328D SER 2.8 29.8 + - - +
330D ARG* 3.5 34.8 - - - +
611D ARG* 3.8 14.6 - - - +
612D LEU* 5.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D PRO* 4.3 14.8 + - + +
144D VAL* 1.3 82.0 - - - +
146D TRP* 1.3 74.1 + - - +
147D ALA* 5.2 1.8 - - + -
325D ARG* 3.7 33.4 - - - +
326D ILE 3.2 5.8 - - - +
327D GLU* 3.9 26.0 - - + +
612D LEU 4.9 3.6 - - - +
613D ARG* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D VAL* 3.7 13.1 - - + +
145D ILE* 1.3 87.8 - - - +
147D ALA* 1.3 60.6 + - - +
309D ASP* 3.9 12.8 - - - -
312D MET* 3.2 49.7 - - + +
313D LEU* 3.5 36.1 - - + -
324D LEU 4.6 0.4 - - - -
325D ARG* 2.8 25.4 - - - +
326D ILE* 2.9 29.1 + - + -
404D HIS* 4.5 14.8 - + + +
405D TYR* 5.1 2.9 - - + -
609D TRP* 4.0 12.1 - + - -
611D ARG* 3.3 28.2 + - - -
612D LEU 4.2 3.6 + - - -
613D ARG 4.0 7.6 - - - +
614D GLY* 3.5 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ILE* 5.2 2.5 - - + -
146D TRP* 1.3 76.9 - - - +
148D ARG* 1.3 61.5 + - - +
149D GLY 4.1 9.1 + - - +
151D VAL* 6.1 1.6 - - + -
324D LEU 3.5 6.5 - - - -
325D ARG* 3.9 18.2 - - + -
404D HIS 5.1 2.9 - - - +
615D GLN* 5.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA* 1.3 74.3 - - - +
149D GLY* 1.3 65.4 + - - +
150D ASP 5.0 0.2 - - - -
151D VAL* 5.0 0.9 + - - +
320D PHE* 3.3 22.7 - - - -
321D VAL 2.6 30.7 + - - +
322D PRO* 3.4 24.1 + - - -
323D ALA* 3.0 23.4 - - - +
324D LEU 2.8 21.0 + - - +
377D TYR* 5.9 0.2 + - - -
402D THR* 2.9 43.4 + - - +
403D THR 3.9 5.8 + - - +
404D HIS* 4.0 37.9 - - + +
406D GLY 5.9 0.2 - - - +
615D GLN* 6.0 3.6 - - - +
----------------------------------------------------------
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