Contacts of the helix formed by residues 340 - 354 (chain H) in PDB entry 3SRF
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 THR 340 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G GLN* 3.2 17.0 - - - +
331G GLU* 4.1 28.5 - - + +
343G GLU* 5.2 2.4 + - - +
332H SER* 3.6 22.2 - - - +
336H LYS* 6.2 2.0 - - + -
338H ARG 5.4 0.7 - - - +
339H PRO* 1.3 76.7 - - - +
341H ARG* 1.3 65.7 + - - +
342H ALA* 4.0 6.1 + - - +
343H GLU* 3.1 32.0 + - - +
344H GLY* 3.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ASP* 4.0 12.9 + - - -
293G ARG* 2.9 58.2 + - + +
294G GLY 3.1 18.8 + - - +
297G GLY* 3.4 19.2 + - - -
298G ILE* 3.5 19.0 - - - +
302G ALA* 5.5 9.8 - - - +
305G VAL* 4.9 8.7 - - + -
327G THR 4.1 3.4 - - - +
328G GLN* 2.8 43.7 + - + +
338H ARG* 5.4 4.8 - - - +
339H PRO 3.4 24.2 + - - -
340H THR* 1.3 72.7 - - - +
342H ALA* 1.3 62.5 + - - +
344H GLY* 3.3 3.0 + - - +
345H SER* 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ARG* 3.9 0.4 - - - +
328G GLN 3.1 23.1 + - - +
329G MET 4.2 0.9 - - - +
342G ALA 4.4 1.3 - - - +
343G GLU* 4.1 24.7 - - + +
346G ASP* 3.4 33.8 - - + +
340H THR* 4.3 4.0 - - - +
341H ARG* 1.3 78.7 - - - +
343H GLU* 1.3 52.7 + - + +
345H SER* 3.1 3.6 + - - -
346H ASP* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G THR* 5.4 4.0 + - - +
342G ALA* 3.7 19.1 - - + -
343G GLU* 5.3 5.4 - - + +
328H GLN 4.8 0.2 - - - +
329H MET 3.2 19.1 - - - +
330H LEU* 3.7 12.3 - - + -
331H GLU* 3.5 12.3 + - - +
332H SER* 2.5 49.4 + - - -
339H PRO* 3.5 6.8 - - - +
340H THR* 3.1 28.6 + - - +
342H ALA* 1.3 76.7 - - + +
344H GLY* 1.3 57.1 + - - +
346H ASP* 3.2 1.4 + - - +
347H VAL* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 344 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G ALA 5.4 8.3 - - - -
303G GLU* 6.2 0.4 - - - -
306G PHE* 5.3 2.1 - - - +
330H LEU* 4.5 1.7 - - - +
339H PRO* 4.8 5.3 - - - +
340H THR 3.1 12.8 + - - -
341H ARG* 3.3 4.2 + - - -
342H ALA 3.3 0.2 - - - -
343H GLU* 1.3 77.3 - - - +
345H SER* 1.3 59.5 + - - +
347H VAL* 3.7 0.5 + - - +
348H ALA* 3.2 20.4 + - - +
380H ILE* 3.7 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ARG* 4.1 9.0 - - - -
306G PHE* 4.5 14.1 - - - -
309G GLN* 4.8 5.6 - - - -
346G ASP* 2.5 34.1 + - - +
349G ASN* 5.8 0.2 - - - +
341H ARG 3.1 10.3 + - - -
342H ALA 3.1 2.4 + - - -
344H GLY* 1.3 73.0 - - - +
346H ASP* 1.3 59.5 + - - +
348H ALA* 3.6 7.4 - - - +
349H ASN* 2.7 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G ALA* 3.3 29.5 - - + +
345G SER* 2.6 27.5 + - - +
346G ASP* 5.4 1.3 - - - +
349G ASN* 5.7 0.2 - - - -
293H ARG* 2.9 34.7 + - - -
309H GLN* 4.9 3.1 + - - -
329H MET* 3.8 15.7 - - - +
342H ALA 2.8 18.7 + - - +
343H GLU 3.2 6.0 + - - +
345H SER* 1.3 77.7 + - - +
347H VAL* 1.3 62.6 + - - +
349H ASN* 3.3 3.4 + - - +
350H ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H MET* 3.8 31.1 - - + +
330H LEU* 3.6 22.9 - - + -
343H GLU 3.0 16.4 + - - +
344H GLY 3.9 0.9 - - - +
346H ASP* 1.3 76.2 - - - +
348H ALA* 1.3 64.6 + - - +
350H ALA* 3.3 2.6 + - - +
351H VAL* 2.9 27.0 + - + +
358H ILE* 3.8 29.3 - - + +
377H GLN* 4.1 9.2 - - + +
380H ILE* 3.8 27.1 - - + -
381H ALA 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G PHE* 3.5 45.1 - - + -
344H GLY 3.2 13.3 + - - +
345H SER 3.3 7.4 + - - +
347H VAL* 1.3 78.7 - - - +
349H ASN* 1.3 57.0 + - - +
351H VAL* 3.3 9.1 - - - +
352H LEU* 2.9 32.2 + - - +
380H ILE* 3.6 12.7 - - + +
384H ALA* 3.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G PHE* 5.7 0.3 - - - +
310G LYS* 3.2 38.8 - - - +
345G SER* 5.7 0.4 - - - +
346G ASP* 5.7 0.2 - - - -
349G ASN* 3.4 47.3 - - - +
353G ASP* 5.1 0.5 - - - +
345H SER* 2.7 36.0 + - - +
346H ASP* 3.9 3.4 - - - +
348H ALA* 1.3 71.8 - - - +
350H ALA* 1.3 56.7 + - - +
352H LEU* 3.1 8.4 + - - +
353H ASP* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H GLN* 4.0 10.1 - - - +
313H ILE* 4.2 1.1 - - - +
325H CYS* 3.9 32.3 - - + -
329H MET* 4.2 9.0 - - + -
346H ASP* 3.0 17.5 + - - +
347H VAL 3.5 5.8 - - - +
349H ASN* 1.3 77.8 - - - +
351H VAL* 1.3 60.2 + - - +
353H ASP* 3.4 16.5 + - - +
355H ALA* 3.4 23.5 + - - +
358H ILE* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H THR* 3.6 16.8 - - + +
347H VAL* 2.9 24.5 - - + +
348H ALA* 3.3 10.3 - - - +
350H ALA* 1.3 73.5 - - - +
352H LEU* 1.3 63.8 + - - +
354H GLY 3.5 1.0 + - - -
355H ALA* 4.5 3.8 - - - +
358H ILE* 5.0 5.1 - - + +
381H ALA* 4.1 14.1 - - + +
384H ALA* 3.6 24.9 - - + -
385H GLU* 3.9 17.5 - - + +
388H MET* 3.5 2.4 - - - +
466H ARG* 2.7 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G PHE* 3.8 19.1 - - + -
310G LYS* 3.7 33.4 - - + +
32H LEU* 6.3 0.2 - - + -
348H ALA 2.9 19.4 + - - +
349H ASN* 3.1 11.9 + - - +
351H VAL* 1.3 75.4 - - - +
353H ASP* 1.3 65.6 + - - +
384H ALA* 3.4 26.0 - - + +
387H ALA* 3.8 9.9 - - + +
388H MET* 3.4 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 6.1 0.5 - - - +
29G MET* 3.9 26.8 - - + +
349G ASN* 5.6 0.2 - - - +
309H GLN* 4.3 12.8 - - - +
310H LYS* 2.7 44.9 + - - +
313H ILE* 3.7 16.5 - - + +
317H ASN* 3.7 9.2 + - - -
349H ASN* 2.8 29.4 + - - +
350H ALA* 3.5 12.2 + - - +
351H VAL 3.3 0.4 - - - -
352H LEU* 1.3 76.4 - - - +
354H GLY* 1.3 57.3 + - - +
388H MET* 5.1 0.9 - - - +
393H LEU* 5.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H ILE* 3.7 3.4 - - - -
317H ASN* 2.9 34.7 - - - +
323H VAL* 3.9 1.6 - - - +
350H ALA 3.5 0.2 + - - -
351H VAL 3.5 1.0 + - - -
352H LEU 3.3 2.9 - - - -
353H ASP* 1.3 80.1 - - - +
355H ALA* 1.3 66.9 + - - +
356H ASP 3.4 2.9 + - - -
388H MET* 4.5 3.1 - - - -
393H LEU* 6.3 0.7 - - - -
444H ARG* 3.2 11.6 + - - -
466H ARG* 3.4 17.5 - - - -
----------------------------------------------------------
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