Contacts of the strand formed by residues 376 - 379 (chain A) in PDB entry 3RCZ
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 ARG 376 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 4.4 2.7 - - - -
373A GLU 5.4 1.8 - - - +
374A ARG* 3.5 13.6 + - - +
375A ILE* 1.3 80.5 - - - +
377A LEU* 1.3 69.8 + - - +
383A TRP* 3.4 70.5 - - + +
384A LEU 5.6 3.6 - - - +
386A PRO* 6.6 0.2 - - + -
403A VAL* 3.7 0.2 - - - -
404A VAL* 2.8 41.5 + - - +
157B PRO* 4.8 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 4.6 4.5 - - + -
356A VAL* 4.0 13.0 - - + +
359A LEU* 3.8 31.9 - - + -
360A ILE* 3.5 33.2 - - + +
363A TYR* 6.1 0.7 - - + -
375A ILE* 5.3 0.2 - - + -
376A ARG* 1.3 80.9 - - - +
378A GLU* 1.3 59.9 + - - +
383A TRP* 3.6 6.6 - - - +
384A LEU* 2.9 41.8 + - + +
401A VAL* 3.5 19.5 - - + -
402A SER 3.3 2.2 - - - +
403A VAL* 3.5 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG 4.2 0.4 - - - -
377A LEU* 1.3 73.7 - - - +
379A PHE* 1.3 62.7 + - - +
380A GLU 3.3 9.9 + - - -
381A GLY* 2.9 32.4 + - - +
382A GLU 3.5 13.9 - - - +
383A TRP* 3.9 22.2 - - + -
400A GLN 4.7 0.3 - - - +
401A VAL* 3.7 4.0 - - - -
402A SER* 2.8 61.2 + - - +
404A VAL* 4.8 3.8 - - + -
20B HIS* 5.1 3.0 + - - -
23B GLY* 4.8 7.7 - - - -
24B PHE 4.2 9.3 - - - +
25B TYR* 3.7 12.5 - - - +
57B LEU* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 4.2 0.4 + - - -
378A GLU* 1.3 76.2 - - - +
380A GLU* 1.3 106.5 + - + +
381A GLY 3.2 0.9 - - - -
382A GLU* 3.0 24.3 + - - +
384A LEU* 4.1 28.6 - - + +
394A GLU* 3.9 25.8 - - + -
395A LEU* 3.6 26.9 - - + -
399A ASP* 3.5 31.0 - - + -
400A GLN 3.6 17.9 - - - +
401A VAL* 4.9 1.6 - - + -
17B ARG* 3.9 17.7 - - + -
20B HIS* 6.2 2.0 - + - -
----------------------------------------------------------
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