Contacts of the strand formed by residues 307 - 316 (chain H) in PDB entry 5FHX
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 TYR 307 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASP 2.9 22.5 + - - -
276H TYR* 3.1 50.4 + - + +
277H PHE* 3.7 31.1 - + - -
278H PRO* 5.4 0.2 - - + -
279H GLU* 3.2 51.2 + - + +
299H ALA* 4.0 7.0 - - + -
300H VAL 3.4 16.8 - - - -
301H LEU* 3.9 31.1 - - + +
302H GLN* 3.6 2.0 - - - -
306H LEU* 1.4 73.7 - - - +
308H SER* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 308 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 3.9 13.5 - - - +
273H VAL 3.3 8.3 + - - -
274H LYS* 3.6 18.0 - - - +
276H TYR* 4.3 2.9 - - - -
299H ALA* 3.3 1.1 - - - -
300H VAL* 2.8 43.7 + - - +
302H GLN* 3.4 26.0 - - - -
307H TYR* 1.3 75.8 - - - +
309H LEU* 1.4 63.1 + - - +
301L THR* 5.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 3.8 1.9 - - - +
273H VAL* 2.8 46.9 + - + +
276H TYR* 3.5 23.8 - - + +
281H VAL* 3.9 20.2 - - + +
283H VAL* 4.5 11.9 - - + -
296H THR* 3.8 19.7 - - + -
297H PHE* 3.5 22.9 - - - +
298H PRO 4.1 2.7 - - - +
299H ALA* 3.8 11.7 - - + +
300H VAL* 5.7 0.4 - - - -
308H SER* 1.4 77.7 + - - +
310H SER* 1.3 79.3 + - - +
311H SER 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 310 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H LEU* 3.8 18.7 - - - +
271H CYS 3.3 6.9 + - - -
272H LEU* 3.4 24.6 - - - +
297H PHE* 3.0 42.6 + - - +
309H LEU* 1.3 76.9 - - - +
311H SER* 1.3 61.7 + - - +
312H VAL* 5.1 2.5 - - - -
256L VAL* 4.3 10.0 - - - +
299L SER* 5.0 12.5 + - - -
301L THR* 4.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H LEU* 4.3 0.3 - - - +
270H GLY* 3.0 4.5 - - - -
271H CYS* 2.9 36.4 + - - -
273H VAL* 5.6 0.2 - - - -
283H VAL* 3.7 28.8 - - - +
285H TRP* 3.0 28.6 + - - -
294H VAL* 4.3 0.9 - - - +
295H HIS 3.4 3.9 + - - -
296H THR* 2.7 25.5 + - - -
309H LEU* 4.3 0.2 - - - +
310H SER* 1.3 74.7 - - - +
312H VAL* 1.4 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H LEU* 4.4 12.1 - - + -
269H LEU 3.4 13.7 - - - +
270H GLY* 4.1 4.5 - - - -
285H TRP* 4.6 2.5 - - - -
294H VAL* 3.2 7.1 - - - +
295H HIS* 2.7 64.5 + - + +
297H PHE* 3.9 7.6 - - + -
310H SER* 5.1 3.1 - - - -
311H SER* 1.4 79.5 + - - +
313H VAL* 1.3 62.9 + - - +
241L PHE* 4.7 7.6 - - + -
256L VAL* 5.8 2.5 - - + -
258L LEU* 3.8 44.6 - - + -
260L ASN* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H ALA 3.8 0.3 - - - +
268H ALA* 3.4 3.0 - - - -
269H LEU* 2.9 53.7 + - + +
285H TRP* 4.0 28.9 - - + -
290H LEU* 3.7 23.6 - - + -
292H SER 3.7 23.1 - - - +
293H GLY 3.4 4.9 - - - -
294H VAL* 3.9 11.4 - - + -
312H VAL* 1.3 77.9 - - - +
314H THR* 1.3 65.8 + - - +
315H VAL* 3.8 15.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 314 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H THR* 4.0 14.7 + - + +
267H ALA 3.1 6.3 - - - +
268H ALA* 3.8 23.8 - - + -
290H LEU* 6.0 0.2 - - - +
292H SER 4.3 2.6 - - - +
293H GLY* 3.3 25.7 + - - +
312H VAL* 5.8 0.9 - - + -
313H VAL* 1.3 77.3 - - - +
315H VAL* 1.3 62.8 + - - +
237L SER* 6.2 0.2 - - - -
239L PHE* 4.1 11.0 - - + -
258L LEU* 4.8 2.0 - - + -
260L ASN* 3.9 35.9 + - - +
261L ASN* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 315 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H THR* 3.7 5.4 + - - -
267H ALA 2.8 36.5 + - - +
269H LEU* 4.1 11.7 - - + -
290H LEU* 4.7 5.6 - - + -
313H VAL* 3.8 21.5 - - + +
314H THR* 1.3 78.0 - - - +
316H PRO* 1.4 71.1 - - + +
319H SER* 3.6 12.6 - - - +
320H LEU* 3.7 20.6 - - + -
325H TYR* 3.5 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 316 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H GLY 3.7 7.4 - - - +
266H THR* 4.8 1.1 - - - -
315H VAL* 1.4 90.5 - - + +
317H SER* 1.4 63.3 + - - +
318H SER* 3.2 16.4 + - - +
319H SER* 2.7 37.7 + - - +
320H LEU* 4.1 0.9 - - - +
325H TYR* 4.9 0.7 - - - +
----------------------------------------------------------
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