Contacts of the strand formed by residues 281 - 288 (chain A) in PDB entry 5C5B
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 ALA 281 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 5.7 8.1 - - + +
280A LYS* 1.3 86.2 + - - +
282A GLY* 1.3 58.7 + - - +
301A PHE* 3.5 22.7 - - + -
302A TYR 3.2 4.9 - - - -
303A PHE* 3.6 15.0 - - + -
366A TRP* 4.1 4.5 - - - -
14B GLN* 4.4 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LYS* 5.9 0.7 - - - -
281A ALA* 1.3 74.1 - - - +
283A TYR* 1.3 62.7 + - - -
284A LEU 3.8 0.2 + - - -
301A PHE* 3.6 17.7 - - - -
302A TYR* 2.8 33.5 + - - +
366A TRP* 3.7 11.8 - - - -
14B GLN* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY* 1.3 71.8 - - - -
284A LEU* 1.3 71.3 + - - +
299A ARG* 3.2 55.6 - - + +
300A GLN* 3.3 20.4 - - - -
301A PHE* 3.7 31.9 - + + -
314A ARG* 3.2 35.5 - - + +
356A GLN 4.6 0.3 - - - +
357A ALA* 5.0 2.1 - - - -
358A GLU* 5.2 4.7 + - - +
362A ASP* 5.6 1.9 - - - +
366A TRP* 5.1 0.2 + - - -
14B GLN* 3.7 14.4 - - + -
15B ASP* 2.5 31.5 + - + -
17B PRO* 3.4 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY 3.8 0.4 + - - +
283A TYR* 1.3 84.1 - - - +
285A ASN* 1.3 67.5 + - - +
298A ASP 3.5 1.0 - - - +
299A ARG* 3.4 2.3 - - - -
300A GLN* 2.9 31.9 + - - +
302A TYR* 3.7 31.5 - - + -
309A LEU* 6.0 0.4 - - + -
342A PHE* 3.8 23.6 - - + -
355A LEU* 4.3 9.2 - - + -
356A GLN 3.4 18.8 - - - +
357A ALA* 3.6 16.6 - - + -
362A ASP* 5.7 0.9 - - + +
366A TRP* 3.4 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 1.3 74.9 - - - +
286A ALA* 1.3 61.2 + - - +
297A TRP* 4.1 27.6 - - + +
298A ASP 3.4 4.9 - - - +
299A ARG* 3.2 34.0 + - - +
338A ARG* 5.2 0.4 - - - -
354A ILE 3.5 1.2 - - - +
355A LEU* 3.2 6.7 - - - -
356A GLN* 2.8 60.4 + - + +
357A ALA 5.6 0.8 + - - -
148B SER* 3.7 20.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU 4.1 0.2 + - - -
285A ASN* 1.3 75.5 - - - +
287A ARG* 1.3 61.1 + - - +
288A ASN* 3.1 17.5 - - - +
297A TRP* 3.6 2.6 - - - -
298A ASP* 3.1 27.8 + - + +
300A GLN* 6.2 1.8 - - - -
302A TYR* 3.2 26.7 - - + +
353A SER* 4.1 11.7 - - - +
354A ILE 3.4 3.8 - - - -
355A LEU* 3.6 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ALA* 1.3 71.8 - - - +
288A ASN* 1.3 62.3 + - - +
289A LYS* 4.5 10.3 + - - +
295A SER* 3.6 21.2 + - - +
296A THR 3.4 7.0 - - - +
297A TRP* 3.4 34.1 - - + +
335A CYS* 3.0 20.6 - - - -
336A GLU* 3.1 26.1 + - - -
353A SER* 3.8 15.8 + - - -
354A ILE* 3.1 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ALA* 3.1 9.9 - - + +
287A ARG* 1.3 75.6 - - - +
289A LYS* 1.3 67.4 + - - +
295A SER* 4.3 2.0 - - - -
296A THR* 3.4 17.9 + - - +
298A ASP* 2.8 31.0 + - - +
353A SER* 4.9 8.1 - - - +
----------------------------------------------------------
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