Contacts of the strand formed by residues 313 - 320 (chain A) in PDB entry 3STJ
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 LYS 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ASN* 4.6 2.3 + - - +
311A GLY 3.7 5.6 + - - +
312A THR* 1.3 82.0 - - - +
314A VAL* 1.3 64.8 + - - +
328A GLU* 3.6 38.0 + - + +
329A VAL 3.3 4.7 - - - +
330A THR* 3.4 29.6 - - - +
120K ASN* 5.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 4.2 4.0 - - + -
290A LEU* 3.8 17.5 - - + -
291A ASN* 3.5 17.5 - - - +
305A ILE* 4.1 6.1 - - + -
308A THR* 4.6 13.0 - - + +
312A THR* 4.7 2.0 - - + -
313A LYS* 1.3 77.3 - - - +
315A LYS* 1.3 61.8 + - - +
316A LEU* 3.9 21.3 - - + -
327A VAL 3.6 0.7 - - - +
328A GLU* 3.3 4.9 - - - -
329A VAL* 2.8 42.4 + - + +
331A LEU* 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A SER 3.9 0.2 - - - +
290A LEU* 3.5 6.6 - - - +
291A ASN* 2.7 47.1 + - - +
314A VAL* 1.3 75.1 - - - +
316A LEU* 1.3 60.5 + - - +
317A GLY 4.0 0.5 + - - -
326A GLU* 3.4 31.7 - - - +
327A VAL 3.4 4.0 - - - +
328A GLU* 3.5 32.7 + - + +
73K SER* 4.9 10.5 + - - +
121K PRO* 3.0 29.1 + - - +
122K SER* 4.7 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 4.1 19.5 - - + -
244A ILE* 5.7 0.2 - - + -
276A SER* 5.0 1.3 - - - +
281A VAL* 4.3 14.8 - - + -
287A ILE* 3.9 38.1 - - + -
289A SER 3.6 2.5 - - - +
290A LEU* 3.9 25.4 - - + -
301A LEU* 5.2 1.1 - - + -
314A VAL* 3.9 17.5 - - + -
315A LYS* 1.3 72.4 - - - +
317A GLY* 1.3 62.6 + - - +
318A LEU* 3.3 9.7 + - + +
325A LEU 3.6 0.3 - - - +
326A GLU* 3.4 6.7 - - - -
327A VAL* 2.7 40.0 + - + +
329A VAL* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ILE* 3.3 7.3 - - - +
288A THR* 2.6 35.7 + - - -
289A SER* 2.9 31.9 + - - -
316A LEU* 1.3 68.2 - - - +
318A LEU* 1.3 56.1 + - - -
325A LEU 3.9 4.0 - - - -
326A GLU* 3.9 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 4.2 18.8 - - + -
285A ASP* 3.3 42.2 - - + +
286A ILE 3.5 8.3 - - - +
287A ILE* 4.5 6.1 - - + +
288A THR* 4.9 2.4 + - - -
316A LEU* 3.9 11.7 - - + +
317A GLY* 1.3 72.9 - - - -
319A LEU* 1.3 76.2 + - - +
320A ARG* 4.1 7.0 - - - +
324A PRO* 3.6 5.7 - - - +
325A LEU* 2.8 63.4 + - + +
327A VAL* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 4.1 29.2 - - + -
260A ASP 5.7 1.1 - - - +
261A VAL* 3.8 28.0 - - + -
284A GLY 4.4 1.0 - - - +
285A ASP* 3.8 2.1 - - - -
286A ILE* 3.0 44.3 + - + +
288A THR* 4.5 7.9 - - + +
318A LEU* 1.3 84.8 - - - +
320A ARG* 1.4 61.0 + - - +
321A ASN 4.2 0.5 + - - -
322A GLY* 4.2 14.0 + - - +
323A LYS 3.5 5.2 - - - +
324A PRO* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 2.6 29.1 + - - -
281A VAL* 4.0 1.0 - - - +
282A LYS* 3.6 34.2 - - - +
284A GLY 5.3 1.8 - - - +
285A ASP* 3.0 43.5 + - - +
318A LEU* 4.1 8.2 - - + +
319A LEU* 1.4 70.9 - - - +
321A ASN* 1.3 72.3 + - + +
322A GLY 3.1 0.9 - - - -
323A LYS* 3.0 31.6 + - + +
325A LEU* 3.7 32.1 - - + +
327A VAL* 5.3 2.4 - - - +
----------------------------------------------------------
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