Contacts of the strand formed by residues 372 - 379 (chain D) in PDB entry 3DLX
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 THR 372 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ARG* 3.9 12.4 + - - +
350D LEU* 3.5 12.1 - - - +
351D GLY* 2.7 34.5 + - - +
352D PRO* 2.6 29.2 + - - +
354D PRO* 3.6 32.8 - - + -
358D GLU* 4.1 14.1 - - + +
363D LEU* 3.8 6.5 - - - -
371D VAL* 1.3 76.4 - - - +
373D ILE* 1.3 66.6 + - - +
374D LEU* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C PRO* 3.8 17.3 - - + -
225D LYS* 6.2 2.5 - - - -
347D VAL* 3.6 31.6 - - + -
349D GLY 3.5 5.2 - - - +
351D GLY 3.9 0.4 - - - +
363D LEU* 3.8 14.9 - - + +
372D THR* 1.3 84.3 - - - +
374D LEU* 1.3 67.5 + - - +
375D PRO* 4.2 2.1 - - - +
377D ALA* 3.6 22.2 - - + -
379D PHE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D VAL 5.1 10.3 - - - +
349D GLY* 2.9 15.8 + - - +
350D LEU 3.5 16.8 - - - +
351D GLY* 3.7 20.6 - - - -
352D PRO* 4.0 11.4 - - + -
372D THR* 5.2 0.9 - - - +
373D ILE* 1.3 77.6 - - - +
375D PRO* 1.4 81.5 - - + +
377D ALA* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ALA* 5.7 0.2 - - - +
251C ILE* 3.6 22.6 - - + +
252C GLY* 5.2 5.8 - - - +
373D ILE 4.4 2.5 - - - +
374D LEU* 1.4 97.7 - - + +
376D GLY* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ASP* 4.4 3.8 - - - -
218C ALA* 4.7 7.0 - - - -
220C ASN* 3.0 31.0 + - - +
251C ILE* 3.5 16.5 - - - +
252C GLY* 4.3 6.6 - - - +
263C GLN* 3.5 15.8 - - - +
349D GLY* 5.9 0.4 - - - -
375D PRO* 1.3 72.1 - - - +
377D ALA* 1.3 63.9 + - - +
378D SER* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C PHE 5.5 0.3 - - - +
256C PRO* 3.3 12.7 - - - +
259C ILE* 3.1 19.1 - - - +
348D LEU 3.2 18.2 - - - +
349D GLY* 3.9 7.4 - - - +
373D ILE* 3.6 35.9 - - + -
374D LEU 3.0 20.2 + - - +
376D GLY* 1.3 78.2 + - - +
378D SER* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ASN* 4.6 2.7 + - - -
256C PRO* 3.4 10.5 - - - -
259C ILE* 3.8 26.2 - - - -
262C PRO* 3.6 23.4 - - - +
263C GLN* 5.5 0.5 + - - -
347D VAL* 3.5 5.4 - - - +
348D LEU* 3.0 41.5 + - - +
376D GLY 5.0 0.5 + - - -
377D ALA* 1.3 74.8 - - - +
379D PHE* 1.3 71.2 + - - +
380D PHE* 3.7 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C PRO* 3.1 46.9 + - + +
257C GLU* 3.9 17.2 - - + +
259C ILE 4.8 6.8 - - - +
225D LYS* 3.5 50.9 - - + +
226D SER 3.7 8.5 - - - -
228D ARG* 3.9 15.2 + - - +
346D GLY 3.2 13.9 - - - +
347D VAL* 3.8 15.3 - - + -
363D LEU* 3.7 25.4 - - + -
373D ILE* 3.7 24.2 - - + -
378D SER* 1.3 77.0 - - - +
380D PHE* 1.3 67.5 + - - +
----------------------------------------------------------
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