Contacts of the strand formed by residues 313 - 322 (chain A) in PDB entry 3HN8
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 GLN 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.3 7.3 - - - -
308A LEU* 3.0 48.6 + - + +
311A SER* 3.2 34.6 + - - +
312A ASP* 1.3 75.0 - - - +
314A LEU* 1.3 63.4 + - - +
315A VAL* 3.5 3.1 + - + -
367A GLN* 3.0 43.3 + - - +
368A PHE 3.1 12.5 + - - +
369A SER* 4.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 4.0 18.6 - - + -
306A ARG 4.0 8.1 - - - +
307A TYR* 3.4 16.6 - - + -
313A GLN* 1.3 69.8 - - - +
315A VAL* 1.3 78.8 + - - +
316A VAL* 4.1 2.9 - - + -
341A LEU* 4.0 15.9 - - + -
367A GLN* 3.6 1.0 - - - -
368A PHE* 2.8 48.5 + - + +
370A VAL* 4.5 7.6 - - + +
375A LEU* 3.8 17.5 - - + -
380A LEU* 4.6 9.4 - - + -
404A LEU* 3.5 35.7 - - + -
408A ALA* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.0 26.7 - - - +
306A ARG* 2.9 42.0 + - + +
308A LEU* 3.8 29.8 - - + -
313A GLN* 4.2 3.1 - - + +
314A LEU* 1.3 74.4 - - - +
316A VAL* 1.3 68.7 + - - +
365A THR* 3.5 26.2 - - + -
366A PHE 3.4 3.8 - - - +
367A GLN* 4.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 5.2 4.5 - - + -
304A ALA 3.7 6.3 - - - +
305A LEU* 4.0 8.7 - - + -
314A LEU* 4.1 9.0 - - + -
315A VAL* 1.3 81.8 - - - +
317A ARG* 1.3 67.2 + - - +
318A ILE* 4.6 6.5 - - + +
339A ILE* 5.3 1.6 - - + -
365A THR* 3.2 4.9 - - - -
366A PHE* 2.8 47.0 + - + +
368A PHE* 4.4 17.0 - - + -
380A LEU* 3.4 26.2 - - + -
382A PHE* 4.0 27.8 - - + -
401A LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 2.8 25.7 - - - +
304A ALA* 2.8 21.6 + - + +
306A ARG* 3.9 26.9 - - - +
315A VAL* 4.8 0.8 - - - +
316A VAL* 1.3 71.4 - - - +
318A ILE* 1.3 61.6 + - - +
319A LEU* 3.5 19.3 + - + +
363A ASN* 3.1 57.7 + - - +
364A GLU 3.3 2.2 - - - +
365A THR* 2.9 46.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
301A ILE* 3.9 17.3 - - + -
302A SER 4.5 0.9 - - - +
303A PHE* 3.8 5.4 - - + -
316A VAL* 3.9 9.6 + - + -
317A ARG* 1.3 72.7 - - - +
319A LEU* 1.3 60.4 + - - +
337A VAL* 3.8 26.2 - - + -
339A ILE* 3.4 33.7 - - + -
351A THR* 4.0 8.7 - - + -
362A PHE* 3.5 33.2 - - + -
363A ASN* 2.9 23.7 + - - -
364A GLU 2.9 17.0 + - - +
366A PHE* 4.4 3.8 - - + -
382A PHE* 4.7 14.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
302A SER* 2.9 20.8 + - - +
303A PHE* 3.5 20.6 - - - +
304A ALA* 4.4 5.8 - - + +
317A ARG* 3.6 41.7 - - + +
318A ILE* 1.3 74.1 - - - +
320A GLN* 1.3 59.8 + - + +
361A ILE* 3.5 1.4 - - - -
362A PHE* 2.8 31.3 + - - -
363A ASN* 3.1 16.7 + - - +
413A ASP* 5.3 6.1 - - - +
415A PRO* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 3.6 5.1 - - - -
302A SER* 2.8 39.7 + - - +
319A LEU* 1.3 85.3 - - + +
321A ALA* 1.3 62.0 + - - +
322A LEU* 3.6 24.8 - - - +
359A ASN* 4.5 1.9 - - - +
360A PRO 3.2 13.5 - - - +
361A ILE* 3.5 30.2 - - + +
362A PHE* 4.3 4.0 - - - +
417A TRP* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG 3.3 11.2 - - - +
301A ILE* 3.9 15.3 - - + +
320A GLN* 1.3 75.2 - - - +
322A LEU* 1.3 75.9 + - - +
324A LEU* 4.0 19.5 - - + -
359A ASN* 3.3 20.1 - - - -
360A PRO* 3.0 28.2 + - + +
362A PHE* 4.5 5.1 - - + -
384A VAL* 6.3 0.4 - - + -
420A ILE* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLY* 3.4 0.2 - - - -
300A ARG* 2.8 62.1 + - - +
320A GLN* 3.6 22.0 - - - +
321A ALA* 1.3 90.1 - - - +
323A ASP* 1.3 73.7 + - - +
324A LEU* 3.0 5.4 + - - +
358A LEU 3.7 0.9 - - - -
359A ASN* 3.5 15.5 - - + +
417A TRP* 3.5 32.1 - - + -
----------------------------------------------------------
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