Contacts of the helix formed by residues 314 - 328 (chain C) in PDB entry 3HTM
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 ALA 314 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.4 10.3 - - + -
286C LYS* 4.5 0.4 - - - +
290C GLU* 3.5 22.2 - - + +
309C ALA* 2.8 26.0 + - + +
312C HIS 4.6 1.6 - - - +
313C SER* 1.3 72.1 - - - +
315C ASP* 1.3 52.6 + - - +
316C GLN 3.4 2.5 - - - -
317C LEU* 3.2 26.0 + - + -
318C LYS* 2.7 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLU* 3.9 2.0 + - - -
313C SER* 3.6 11.5 + - - +
314C ALA* 1.3 72.9 - - - +
316C GLN* 1.3 67.9 + - + +
318C LYS* 3.5 8.1 - - - +
319C THR* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 4.0 12.9 - - + +
290C GLU* 3.2 11.9 + - - +
315C ASP* 1.3 81.1 - - + +
317C LEU* 1.3 60.7 + - - +
319C THR* 4.0 4.5 - - - -
320C GLN* 3.1 32.4 + - + +
178D MSE 4.1 1.9 - - - +
179D VAL* 3.1 20.5 - - + -
180D LYS* 2.5 56.1 + - - +
182D PRO* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 4.0 8.7 - - + -
290C GLU* 2.7 40.7 + - + +
293C LEU* 3.9 25.8 - - + -
294C CYS* 4.0 17.3 - - + +
297C LEU* 5.3 2.9 - - + -
305C ILE* 3.7 26.7 - - + +
308C LEU* 4.9 0.7 - - + -
309C ALA* 3.6 22.7 - - + +
314C ALA* 3.5 20.0 - - + -
315C ASP 3.1 0.4 - - - -
316C GLN* 1.3 71.0 - - - +
318C LYS* 1.3 60.5 + - - +
320C GLN* 3.4 4.1 + - - +
321C ALA* 2.9 29.6 + - - +
179D VAL* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 2.7 40.9 + - - +
318B LYS* 2.6 42.0 - - - +
306C LEU* 3.9 9.6 - - + -
309C ALA* 3.6 15.7 - - + +
310C ASP* 3.3 6.1 - - - +
314C ALA 2.7 21.7 + - - +
315C ASP* 3.5 8.3 - - - +
317C LEU* 1.3 71.6 - - - +
319C THR* 1.3 59.1 + - - +
321C ALA* 2.7 26.5 + - - +
322C VAL* 2.8 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ASP* 2.9 18.5 + - - +
316C GLN* 4.0 5.8 - - - -
318C LYS* 1.3 79.1 - - - +
320C GLN* 1.3 67.1 + - - +
322C VAL* 3.4 5.8 + - - +
323C ASP* 3.0 50.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
294C CYS* 3.7 27.5 - - - -
297C LEU* 3.9 6.1 - - + +
316C GLN* 3.1 20.5 + - + +
317C LEU 3.7 3.8 - - - +
318C LYS 3.2 0.8 - - - -
319C THR* 1.3 87.5 - - - +
321C ALA* 1.3 57.9 + - - +
323C ASP* 4.0 10.6 + - - +
324C PHE* 3.1 27.2 + - - +
178D MSE 2.9 47.4 + - + +
179D VAL* 4.4 5.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
297C LEU* 4.3 19.3 - - + -
302C ALA 4.8 2.0 - - - +
305C ILE* 4.7 3.1 - - + -
306C LEU* 4.0 33.4 - - + +
317C LEU 2.9 13.6 + - - +
318C LYS* 2.7 19.4 + - - +
320C GLN* 1.3 70.7 - - - +
322C VAL* 1.3 61.9 + - - +
324C PHE* 3.4 2.4 + - - +
325C ILE* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASP* 3.9 39.9 - - + +
311B LEU* 4.1 16.8 - - + +
306C LEU* 4.1 9.4 - - + -
318C LYS* 2.8 29.4 + - + +
319C THR* 3.8 7.4 - - - +
321C ALA* 1.3 70.5 - - - +
323C ASP* 1.3 65.5 + - - +
324C PHE 3.3 0.2 + - - -
325C ILE* 3.3 4.0 + - - +
326C ASN* 2.9 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C THR* 3.0 31.7 + - - +
320C GLN* 4.0 13.8 + - - +
322C VAL* 1.3 82.5 - - - +
324C PHE* 1.3 61.2 + - - +
326C ASN* 3.8 8.6 + - - +
327C TYR* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 3.8 30.1 - - + -
298C SER* 3.3 44.4 - - - -
299C VAL* 3.5 8.7 - - + -
302C ALA* 3.6 19.5 - - + -
320C GLN 3.1 19.7 + - - +
321C ALA* 3.5 5.6 - - - +
322C VAL 3.2 0.2 - - - -
323C ASP* 1.3 78.9 - - - +
325C ILE* 1.3 67.5 + - - +
327C TYR* 3.5 3.1 - - - +
328C HIS* 3.0 61.2 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 5.1 4.9 - - + -
311B LEU* 4.0 25.6 - - + -
302C ALA* 3.8 33.7 - - + +
303C ALA* 4.4 6.5 - - + +
306C LEU* 3.8 28.5 - - + -
321C ALA 3.0 16.6 + - - +
322C VAL 3.7 3.8 - - - +
324C PHE* 1.3 80.6 - - - +
326C ASN* 1.3 67.5 + - - +
328C HIS* 3.2 20.3 + - - +
329C ALA* 3.7 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.9 24.1 + - - +
322C VAL* 2.9 44.9 + - - +
323C ASP* 3.8 8.4 + - - +
325C ILE* 1.3 72.8 - - - +
327C TYR* 1.3 65.5 + - - +
329C ALA* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C ASP 3.0 16.5 + - - +
324C PHE* 3.5 5.4 - - - +
326C ASN* 1.3 78.7 - - - +
328C HIS* 1.3 84.7 + + - +
329C ALA* 2.9 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C VAL* 4.1 26.1 - - + +
324C PHE* 3.0 70.4 + + + +
325C ILE* 3.5 10.3 - - - +
326C ASN 3.1 0.6 + - - -
327C TYR* 1.3 98.2 - + - +
329C ALA* 1.3 59.4 + - - +
----------------------------------------------------------
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