Contacts of the strand formed by residues 377 - 384 (chain A) in PDB entry 4GB1
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 SER 377 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 3.9 0.9 - - - -
371A ILE* 3.2 14.6 + - - +
372A SER* 3.2 28.8 + - - -
375A SER* 3.1 10.0 + - - -
376A ARG* 1.3 76.1 - - - +
378A GLY* 1.3 69.7 + - - +
405A ASN* 4.2 17.1 + - - +
407A ASN 3.5 9.9 - - - -
408A TRP* 3.7 22.0 - - - -
409A SER* 3.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 3.3 4.9 - - - -
371A ILE* 3.2 17.0 + - - -
377A SER* 1.3 79.3 - - - +
379A PHE* 1.3 61.1 + - - +
403A VAL* 3.0 16.6 - - - -
404A ASP 3.4 16.3 + - - -
405A ASN* 4.1 0.7 - - - -
407A ASN 2.6 15.8 + - - -
409A SER* 2.9 19.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
355A LYS 6.0 0.2 - - - -
356A GLY* 6.0 1.6 - - - -
357A PHE* 3.3 32.5 - + - -
368A GLY* 3.8 1.8 - - - -
369A ARG* 3.6 33.0 - - - -
370A THR* 4.3 3.6 - - + -
371A ILE* 3.5 3.0 - - - +
378A GLY* 1.3 75.5 - - - +
380A GLU* 1.3 84.5 + - - +
401A VAL* 3.6 1.7 - - - +
402A VAL* 2.9 31.9 + - + -
403A VAL* 2.6 29.6 + - + +
409A SER* 4.4 5.2 - - - -
410A GLY 4.8 5.8 - - - -
412A SER* 2.9 29.8 - - - -
432A PHE* 4.0 10.3 - + - -
434A VAL* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG* 4.9 0.5 + - - -
367A MET 4.0 0.7 - - - +
368A GLY* 3.3 2.8 - - - -
369A ARG* 3.0 75.2 + - + +
370A THR 4.4 1.9 - - - +
371A ILE* 3.8 27.6 - - + +
379A PHE* 1.3 82.4 - - - +
381A ILE* 1.3 61.3 + - - +
382A LEU* 4.3 16.0 - - + +
399A LYS* 3.0 28.7 + - + +
400A GLN 3.7 10.8 - - - +
401A VAL* 4.2 8.3 - - + +
402A VAL* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 3.4 37.0 - - + -
357A PHE* 3.5 34.1 - - + -
366A TRP* 3.4 32.2 - - + -
367A MET 3.5 19.7 - - - +
368A GLY* 4.5 0.9 - - - -
379A PHE* 5.0 0.9 - - + -
380A GLU* 1.3 76.9 - - - +
382A LEU* 1.3 60.4 + - - +
399A LYS* 3.5 0.7 - - - -
400A GLN* 3.2 42.5 + - + +
402A VAL* 5.6 1.3 - - + +
432A PHE* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 4.4 13.5 - - + -
332A ASP* 5.2 0.7 - - - +
365A VAL 3.4 1.0 - - - +
366A TRP* 3.4 3.9 - - - -
367A MET* 2.8 44.4 + - + +
369A ARG* 4.1 33.2 - - - +
380A GLU* 4.3 15.3 - - + +
381A ILE* 1.3 74.6 - - - +
383A ARG* 1.3 59.8 + - - +
384A ILE* 3.9 20.4 - - + -
395A GLN* 3.5 20.2 - - - +
397A ARG 3.4 4.0 - - - +
399A LYS* 3.6 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 2.7 38.1 + - - -
94A ALA 3.4 10.1 + - - -
95A LYS* 4.9 1.4 - - - +
361A GLN* 3.3 18.5 + - - +
364A ASP* 3.2 32.8 + - + +
365A VAL 3.2 12.1 - - - +
366A TRP* 3.3 49.1 - - + +
382A LEU* 1.3 71.7 - - - +
384A ILE* 1.3 59.3 + - - +
395A GLN* 3.6 2.4 - - - -
396A ILE* 2.9 45.8 + - + +
397A ARG* 2.7 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ALA* 4.0 3.1 - - + -
323A ILE* 3.7 24.0 - - + -
364A ASP* 3.2 3.9 - - - +
365A VAL* 3.0 37.2 + - + -
367A MET* 4.1 28.9 - - + -
382A LEU* 4.1 13.9 - - + -
383A ARG* 1.3 77.7 - - - +
385A LYS* 1.3 67.9 + - - +
386A ASN 3.2 1.4 + - - -
387A GLY* 3.3 7.5 + - - -
392A SER* 3.4 39.0 - - - +
393A LYS* 4.2 0.4 - - - -
394A GLU 3.4 6.3 - - - +
395A GLN* 4.0 18.2 - - + +
396A ILE* 4.6 0.2 - - - -
----------------------------------------------------------
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