Contacts of the strand formed by residues 313 - 322 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.2 7.8 - - - -
308C LEU* 3.0 47.8 + - + +
311C SER* 3.2 34.6 + - - +
312C ASP* 1.3 74.2 - - - +
314C LEU* 1.3 63.0 + - - +
315C VAL* 3.5 2.9 + - + -
367C GLN* 3.0 44.4 + - - +
368C PHE 3.1 12.9 + - - +
369C SER* 4.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 4.0 18.8 - - + -
306C ARG 4.0 8.5 - - - +
307C TYR* 3.5 16.3 - - + -
313C GLN* 1.3 70.2 - - - +
315C VAL* 1.3 77.2 + - - +
316C VAL* 4.1 3.6 - - + -
341C LEU* 4.0 15.7 - - + -
367C GLN* 3.6 1.0 - - - -
368C PHE* 2.8 49.7 + - + +
370C VAL* 4.5 7.8 - - + +
375C LEU* 3.8 18.2 - - + -
380C LEU* 4.6 8.7 - - + -
404C LEU* 3.5 36.3 - - + -
408C ALA* 5.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 3.0 27.2 - - - +
306C ARG* 2.9 42.0 + - + +
308C LEU* 3.8 30.7 - - + -
313C GLN* 4.3 2.0 - - + +
314C LEU* 1.3 75.1 - - - +
316C VAL* 1.3 69.4 + - - +
365C THR* 3.5 26.0 - - + -
366C PHE 3.3 3.6 - - - +
367C GLN* 4.3 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PHE* 5.2 4.9 - - + -
304C ALA 3.7 5.8 - - - +
305C LEU* 4.0 9.0 - - + -
314C LEU* 4.1 9.0 - - + -
315C VAL* 1.3 81.7 - - - +
317C ARG* 1.3 69.4 + - - +
318C ILE* 4.6 6.7 - - + +
339C ILE* 5.3 1.3 - - + -
365C THR* 3.3 5.0 - - - -
366C PHE* 2.8 45.4 + - + +
368C PHE* 4.4 17.3 - - + -
380C LEU* 3.4 26.2 - - + -
382C PHE* 4.0 27.4 - - + -
401C LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C PHE* 2.8 25.6 - - - +
304C ALA* 2.8 23.0 + - + +
306C ARG* 3.9 26.7 - - - +
315C VAL* 4.3 0.8 - - - +
316C VAL* 1.3 70.5 - - - +
318C ILE* 1.3 60.6 + - - +
319C LEU* 3.5 19.4 + - + +
363C ASN* 3.1 57.7 + - - +
364C GLU 3.3 2.2 - - - +
365C THR* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 3.9 17.5 - - + -
302C SER 4.5 0.9 - - - +
303C PHE* 3.9 4.9 - - + -
316C VAL* 3.8 10.0 + - + -
317C ARG* 1.3 70.8 - - - +
319C LEU* 1.3 60.9 + - - +
337C VAL* 3.8 26.2 - - + -
339C ILE* 3.4 33.9 - - + -
351C THR* 4.0 9.0 - - + -
362C PHE* 3.6 34.0 - - + +
363C ASN* 2.9 23.0 + - - -
364C GLU 2.9 17.8 + - - +
366C PHE* 4.4 4.0 - - + -
382C PHE* 4.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C SER* 2.9 21.2 + - - +
303C PHE* 3.5 19.3 - - - -
304C ALA* 4.7 5.8 - - + +
317C ARG* 3.6 40.8 - - + +
318C ILE* 1.3 73.5 - - - +
320C GLN* 1.3 67.9 + - + +
361C ILE* 3.5 1.2 - - - +
362C PHE* 2.7 27.1 + - - -
363C ASN* 3.2 15.1 + - - +
415C PRO* 3.8 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 3.6 4.7 - - - -
302C SER* 2.8 43.6 + - - +
319C LEU* 1.3 86.1 - - + +
321C ALA* 1.3 60.5 + - - +
322C LEU* 3.6 24.3 - - - +
359C ASN* 4.5 1.9 - - - +
360C PRO 3.2 13.6 - - - +
361C ILE* 3.5 30.0 - - + +
362C PHE* 4.4 4.0 - - - +
417C TRP* 3.9 17.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ARG 3.3 12.1 - - - +
301C ILE* 3.9 15.5 - - + +
320C GLN* 1.3 73.9 - - - +
322C LEU* 1.3 75.8 + - - +
324C LEU* 4.0 19.7 - - + -
359C ASN* 3.3 19.3 - - - -
360C PRO* 3.0 27.3 + - + +
362C PHE* 4.5 4.8 - - + -
384C VAL* 6.3 0.4 - - + -
420C ILE* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C GLY* 3.4 0.2 - - - -
300C ARG* 2.8 62.3 + - - +
320C GLN* 3.6 21.8 - - - +
321C ALA* 1.3 89.8 - - - +
323C ASP* 1.3 73.9 + - - +
324C LEU* 3.0 5.9 + - - +
358C LEU 3.7 0.7 - - - -
359C ASN* 3.5 15.9 - - + +
417C TRP* 3.5 31.6 - - + -
----------------------------------------------------------
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