Contacts of the strand formed by residues 368 - 372 (chain A) in PDB entry 3NBN
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 LEU 368 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PRO* 3.3 29.6 - - + -
364A PHE* 5.7 0.7 - - - -
365A THR* 2.7 53.6 - - - +
366A PRO 3.1 4.1 + - - +
367A ASN* 1.3 90.9 - - - +
369A ARG* 1.3 86.9 + - - +
379A THR* 4.0 7.2 - - - +
387A MET* 4.6 13.7 - - + -
414A LEU* 3.5 30.5 - - + -
415A VAL 3.3 11.7 - - - +
416A ARG* 4.6 6.1 - - + -
417A ASN* 5.8 0.7 - - - -
422A TYR* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 4.9 11.9 - - - +
366A PRO 3.0 13.7 + - - -
368A LEU* 1.3 99.1 + - - +
370A VAL* 1.3 65.4 + - - +
371A TRP* 3.2 13.3 - - - +
376A GLU* 3.8 33.4 - - + +
377A ALA 4.0 7.9 - - - +
378A GLU* 5.3 0.9 - - - +
379A THR* 3.4 28.4 - - - +
387A MET* 5.2 0.6 - - - +
414A LEU* 4.9 1.1 - - - -
415A VAL 3.3 20.1 + - - +
417A ASN* 4.4 11.5 + - - -
34C HIS* 3.5 10.2 + - - -
38C GLU* 2.6 41.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 5.0 0.2 - - + -
359A LEU* 4.1 7.9 - - + -
369A ARG* 1.3 72.9 - - - +
371A TRP* 1.3 59.3 + - - +
372A PHE* 3.5 25.8 - - + -
377A ALA* 3.3 27.7 + - - +
379A THR* 2.9 16.5 + - + +
387A MET* 3.9 21.5 - - + -
388A LEU 5.3 0.9 - - - -
389A CYS* 3.4 24.7 - - + -
412A VAL* 3.8 21.8 - - + -
413A THR 3.5 4.9 - - - +
414A LEU* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 5.1 1.6 - - - -
17A LEU* 3.4 33.4 - - + -
18A THR 3.9 0.7 - - - -
19A ARG* 3.9 21.1 - - - -
22A MET* 3.7 27.4 - - + -
369A ARG 3.2 22.4 + - - -
370A VAL* 1.3 73.7 - - - +
372A PHE* 1.3 62.4 + - - +
373A GLY 3.5 9.8 + - - +
374A ASP* 2.9 39.9 - - - -
375A VAL 3.7 2.9 - - - -
376A GLU* 2.5 47.6 + - + -
411A PRO 3.5 0.7 - - - +
412A VAL* 3.5 1.9 - - - -
413A THR* 2.8 41.0 + - + +
415A VAL* 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.5 24.2 - - + -
370A VAL* 3.5 20.6 - - + -
371A TRP* 1.3 73.7 - - - +
373A GLY* 1.3 63.1 + - - +
374A ASP 3.0 4.7 + - - -
375A VAL 3.0 19.3 + - - +
377A ALA* 3.6 28.5 - - + -
389A CYS* 3.8 7.9 - - - -
391A VAL* 4.0 13.0 - - + -
392A PRO* 3.6 27.4 - - + -
397A PHE* 3.2 24.9 - - + -
410A VAL* 3.5 12.8 - - + -
411A PRO 4.1 1.6 - - - -
412A VAL* 4.7 5.2 - - + +
428A PHE* 3.8 40.2 - + + -
430A TYR* 4.5 5.2 - - - -
----------------------------------------------------------
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