Contacts of the strand formed by residues 385 - 390 (chain A) in PDB entry 3SWD
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 GLY 385 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL 3.7 0.9 - - - +
7A GLN* 3.7 5.7 - - - -
8A GLY* 2.8 40.3 + - - -
362A GLY* 4.6 1.6 - - - -
380A GLY 5.0 1.2 - - - +
383A ALA 4.2 1.0 - - - +
384A GLU* 1.3 82.3 + - - +
386A THR* 1.3 62.5 + - - -
387A THR* 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.9 25.1 - - + -
6A VAL 3.3 9.0 - - - +
7A GLN* 2.7 29.7 + - - +
362A GLY* 3.4 18.8 - - - -
363A ALA* 3.4 2.6 + - - -
384A GLU 4.3 0.4 + - - -
385A GLY* 1.3 72.9 - - - -
387A THR* 1.3 67.4 + - - +
388A VAL* 4.4 8.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE 3.5 1.7 - - - +
5A ARG* 3.6 2.1 - - - -
6A VAL* 2.8 40.1 + - + +
341A MET* 3.6 18.6 - - + +
362A GLY* 3.2 20.6 - - - -
363A ALA 3.3 15.7 - - - +
365A VAL* 4.2 10.5 - - + -
376A LEU 4.7 0.9 - - - +
380A GLY* 3.7 25.1 + - - -
383A ALA* 4.2 2.6 - - - +
385A GLY 4.1 0.9 + - - -
386A THR* 1.3 72.0 - - - +
388A VAL* 1.3 65.7 + - - +
389A VAL* 4.1 20.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 4.0 32.8 - - + +
4A PHE 3.4 7.2 - - - +
5A ARG* 4.7 13.2 - - + +
363A ALA 3.2 7.3 + - - -
364A GLN* 3.5 23.7 - - + +
365A VAL 2.9 26.5 + - - +
386A THR* 4.4 13.9 + - + +
387A THR* 1.3 77.1 - - - +
389A VAL* 1.3 63.4 + - - +
390A ASP* 3.7 3.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.6 1.6 - - - -
4A PHE* 2.9 45.5 + - + +
6A VAL* 4.9 4.5 - - + -
365A VAL* 3.5 19.3 - - + +
367A ALA* 4.3 13.2 - - + +
376A LEU* 4.1 35.4 - - + +
377A VAL* 4.3 9.2 - - + +
387A THR* 4.1 8.1 - - + -
388A VAL* 1.3 73.5 - - - +
390A ASP* 1.3 69.3 + - - +
392A ILE* 3.3 18.4 - - + +
395A ILE* 4.7 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.5 11.4 - - - +
2A ASP 3.9 1.7 - - - +
3A LYS* 3.3 41.8 + - + +
365A VAL 2.8 16.4 + - - +
366A MET* 4.8 11.2 - - + +
367A ALA* 3.1 24.3 + - - +
388A VAL* 3.7 4.8 + - + +
389A VAL* 1.3 74.7 - - - +
391A ARG* 1.3 94.9 + - + +
392A ILE 3.4 0.7 + - - -
84B TYR* 5.3 8.1 + - + +
88B LYS* 4.6 12.8 + - - -
----------------------------------------------------------
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