Contacts of the strand formed by residues 313 - 322 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TYR* 3.2 8.3 - - - -
308B LEU* 3.0 48.9 + - + +
311B SER* 3.2 34.2 + - - +
312B ASP* 1.3 75.0 - - - +
314B LEU* 1.3 63.0 + - - +
315B VAL* 3.5 2.5 + - + -
367B GLN* 3.0 43.1 + - - +
368B PHE 3.1 12.7 + - - +
369B SER* 4.7 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.0 18.4 - - + -
306B ARG 4.0 8.1 - - - +
307B TYR* 3.4 17.1 - - + -
313B GLN* 1.3 70.5 - - - +
315B VAL* 1.3 77.0 + - - +
316B VAL* 4.1 3.4 - - + -
341B LEU* 4.0 16.2 - - + -
367B GLN* 3.6 1.2 - - - -
368B PHE* 2.8 49.2 + - + +
370B VAL* 4.5 7.6 - - + +
375B LEU* 3.8 17.3 - - + -
380B LEU* 4.6 8.5 - - + -
404B LEU* 3.5 36.3 - - + -
408B ALA* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.0 27.4 - - - +
306B ARG* 2.9 41.6 + - + +
308B LEU* 3.8 31.4 - - + -
313B GLN* 3.5 2.0 + - + +
314B LEU* 1.3 75.6 - - - +
316B VAL* 1.3 68.4 + - - +
365B THR* 3.5 25.8 - - + -
366B PHE 3.3 4.0 - - - +
367B GLN* 4.3 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 5.2 4.7 - - + -
304B ALA 3.7 5.6 - - - +
305B LEU* 4.0 10.1 - - + -
314B LEU* 4.1 8.3 - - + -
315B VAL* 1.3 82.3 - - - +
317B ARG* 1.3 67.1 - - - +
318B ILE* 4.6 6.5 - - + +
339B ILE* 5.3 1.1 - - + -
365B THR* 3.3 4.6 - - - -
366B PHE* 2.8 47.1 + - + +
368B PHE* 4.4 17.5 - - + -
380B LEU* 3.4 26.9 - - + -
382B PHE* 4.0 26.7 - - + -
401B LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 2.8 24.9 - - - +
304B ALA* 2.8 23.6 + - + +
306B ARG* 3.9 26.9 - - - +
315B VAL* 4.3 1.0 - - - +
316B VAL* 1.3 70.1 - - - +
318B ILE* 1.3 61.1 + - - +
319B LEU* 3.5 20.3 + - + +
363B ASN* 3.1 57.0 + - - +
364B GLU 3.3 2.2 - - - +
365B THR* 2.9 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 4.0 17.5 - - + -
302B SER 4.5 1.1 - - - +
303B PHE* 3.8 5.4 - - + -
316B VAL* 3.9 9.8 + - + -
317B ARG* 1.3 72.1 - - - +
319B LEU* 1.3 61.4 + - - +
337B VAL* 3.8 26.5 - - + -
339B ILE* 3.4 33.9 - - + -
351B THR* 4.0 8.5 - - + -
362B PHE* 3.5 32.8 - - + -
363B ASN* 2.9 23.4 + - - -
364B GLU 2.9 17.7 + - - +
366B PHE* 4.4 3.6 - - + -
382B PHE* 4.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B SER* 2.9 21.2 + - - +
303B PHE* 3.5 20.0 - - - +
304B ALA* 4.4 6.5 - - + +
317B ARG* 3.6 41.3 - - + +
318B ILE* 1.3 73.7 - - - +
320B GLN* 1.3 59.9 + - + +
361B ILE* 3.5 1.7 - - - -
362B PHE* 2.7 32.4 + - - -
363B ASN* 3.2 14.9 + - - +
415B PRO* 3.8 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 3.6 4.6 - - - -
302B SER* 2.8 39.0 + - - +
319B LEU* 1.3 86.3 - - + +
321B ALA* 1.3 61.4 + - - +
322B LEU* 3.6 25.5 - - - +
359B ASN* 4.5 2.3 - - - +
360B PRO 3.2 13.0 - - - +
361B ILE* 3.5 29.2 - - + +
362B PHE* 4.3 4.4 - - - +
417B TRP* 3.9 16.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG 3.3 11.0 - - - +
301B ILE* 3.9 15.9 - - + +
320B GLN* 1.3 76.2 - - - +
322B LEU* 1.3 75.6 + - - +
324B LEU* 4.0 19.3 - - + -
359B ASN* 3.3 19.4 - - - +
360B PRO* 3.0 27.9 + - + +
362B PHE* 4.5 4.8 - - + -
384B VAL* 6.3 0.7 - - + -
420B ILE* 4.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLY* 3.4 0.3 - - - -
300B ARG* 2.8 60.6 + - - +
320B GLN* 3.6 22.0 - - - +
321B ALA* 1.3 89.9 - - - +
323B ASP* 1.3 73.6 + - - +
324B LEU* 3.0 5.2 + - - +
358B LEU 3.7 0.9 - - - -
359B ASN* 3.5 15.3 - - + +
417B TRP* 3.5 32.5 - - + -
----------------------------------------------------------
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