Contacts of the strand formed by residues 317 - 326 (chain A) in PDB entry 3HO5
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 HIS 317 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.6 18.3 - - + +
304A THR* 3.1 30.6 + - + +
305A THR 3.4 15.0 - - - +
306A ASN* 3.5 9.4 - - - +
315A HIS* 3.6 10.9 + - - +
316A ASP* 1.3 108.3 - - + +
318A ILE* 1.3 65.0 + - - +
319A LEU* 5.0 2.0 - - - -
347A GLU* 2.7 52.7 + - + +
349A HIS 3.2 19.5 + - - -
350A ARG* 4.4 0.2 - - - -
353A LEU* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 3.1 44.8 + - + +
306A ASN 4.8 7.0 - - - +
309A ARG 6.1 0.7 - - - +
310A TRP* 3.7 52.9 - - + +
315A HIS* 4.5 4.0 - - + +
317A HIS* 1.3 85.8 - - - +
319A LEU* 1.3 63.9 + - - +
320A ARG* 3.4 9.2 + - + +
344A GLU* 3.9 22.9 - - + +
345A VAL 3.4 10.5 - - - +
346A ALA* 3.5 20.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
285A LEU* 3.6 27.6 - - + -
302A SER* 4.5 9.4 - - - -
303A TYR 3.6 3.8 - - - +
304A THR* 4.6 7.0 - - - +
317A HIS* 4.3 4.3 + - + +
318A ILE* 1.3 68.8 - - - +
320A ARG* 1.3 74.1 - - - +
321A VAL* 4.3 9.6 - - + -
343A LEU 3.9 0.7 - - - +
344A GLU* 3.6 1.0 - - - -
345A VAL* 2.7 50.8 + - + +
347A GLU* 4.0 15.4 + - + +
353A LEU* 3.8 25.1 - - + +
354A GLY 4.4 1.8 - - - +
355A GLY* 4.4 0.9 - - - -
369A LEU* 3.7 33.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
271A LEU* 5.2 9.9 - - - +
301A VAL 4.4 0.2 - - - -
302A SER* 3.2 5.2 - - - -
303A TYR* 2.7 70.7 + - + +
305A THR* 3.5 37.3 + - + +
306A ASN 5.4 2.6 + - - -
309A ARG 5.7 3.8 - - - +
318A ILE* 3.4 8.0 + - + +
319A LEU* 1.3 76.2 - - - +
321A VAL* 1.3 68.5 + - - +
322A VAL* 3.6 17.0 - - + -
341A VAL* 3.8 17.2 - - + +
343A LEU 3.4 10.3 - - - +
344A GLU* 3.3 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 5.3 2.2 - - + -
301A VAL 3.3 7.4 - - - +
302A SER* 4.1 13.7 - - - -
319A LEU* 4.3 9.9 - - + +
320A ARG* 1.3 78.4 - - - +
322A VAL* 1.3 60.3 + - - +
341A VAL* 3.9 0.3 - - - -
342A PHE* 2.7 50.0 + - + +
343A LEU* 2.8 33.8 + - + +
345A VAL* 6.1 1.3 - - + -
357A LEU* 4.3 23.6 - - + -
365A LEU* 5.0 7.4 - - + -
367A ILE* 4.5 19.1 - - + -
369A LEU* 5.7 0.2 - - + -
395A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 3.4 7.6 - - - +
301A VAL* 2.8 34.4 + - + +
303A TYR* 3.6 20.2 - - + +
320A ARG* 3.6 30.5 - - + -
321A VAL* 1.3 79.9 - - - +
323A GLU* 1.3 68.3 + - - +
324A TYR* 3.7 25.2 + - + +
339A ALA* 3.8 8.5 - - + -
340A ARG 3.4 26.9 - - - +
341A VAL* 4.1 9.4 - - + +
342A PHE* 5.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS* 2.7 28.7 + - + +
299A LEU 3.4 13.9 - - - +
300A TYR* 2.8 38.3 + - + -
322A VAL* 1.3 72.8 - - - +
324A TYR* 1.3 71.3 + - - +
325A THR* 4.9 0.2 - - - +
338A THR 3.1 9.5 - - - +
339A ALA* 3.5 2.4 - - - -
340A ARG* 2.6 79.1 + - + +
342A PHE* 3.7 14.0 - - + -
619A PRO* 3.9 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.5 3.4 - - + -
268A ILE* 3.1 38.7 - - + +
271A LEU* 3.7 12.5 - - - +
298A LYS* 3.5 3.8 - - - -
299A LEU* 2.8 50.1 + - + +
301A VAL* 4.1 19.7 - - + -
303A TYR* 4.6 2.4 + + - -
322A VAL* 3.7 19.5 + - + -
323A GLU* 1.3 78.5 - - - +
325A THR* 1.3 66.6 + - - +
334A VAL* 3.8 22.0 - - + -
335A ASP 4.0 0.9 - - - -
336A LEU* 3.5 36.7 + - + +
338A THR* 3.8 12.1 - - - -
339A ALA* 3.6 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASN 3.8 14.1 - - - +
297A GLY 3.3 16.4 - - - +
298A LYS* 2.8 29.6 + - - +
299A LEU* 3.9 4.9 - - - -
323A GLU* 4.5 0.2 + - - -
324A TYR* 1.3 75.8 + - - +
326A VAL* 1.3 73.1 + - - +
334A VAL* 3.5 1.7 - - - +
335A ASP* 3.3 18.7 + - - +
338A THR* 3.1 33.3 + - + +
604A LEU* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.5 19.7 - - + +
293A TYR* 3.1 28.3 - - + +
297A GLY* 3.1 32.3 + - - +
299A LEU* 3.9 2.4 - - - +
325A THR* 1.3 78.2 - - - +
327A SER* 1.3 68.1 + - - +
328A ARG* 3.2 4.7 + - - +
330A ASN 4.2 2.2 - - - +
331A PRO* 3.9 14.8 - - + +
333A GLN 3.6 13.0 - - - +
334A VAL* 3.7 4.9 - - - +
335A ASP* 4.3 2.6 - - - +
604A LEU* 3.8 24.9 - - + +
----------------------------------------------------------
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