Contacts of the helix formed by residues 315 - 327 (chain D) in PDB entry 1T9D
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 ASP 315 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D HIS* 2.9 23.9 + - + +
314D ALA* 1.3 82.0 - - - +
316D GLY* 1.3 65.7 + - - +
317D PRO 3.5 1.1 - - - -
318D ARG* 2.7 49.8 + - - +
319D LEU* 3.0 26.8 + - + +
428D THR* 3.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 3.2 22.2 - - - +
313D HIS 3.0 8.7 + - - -
315D ASP* 1.3 77.7 - - - +
317D PRO* 1.3 68.8 - - - +
319D LEU* 3.3 1.6 + - - +
320D LEU* 2.9 23.0 + - - +
428D THR* 3.1 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 3.8 9.9 - - + +
311D LEU* 4.2 11.2 - - + -
313D HIS 3.9 6.3 - - - +
314D ALA 3.9 8.3 - - - +
315D ASP 3.8 2.2 - - - -
316D GLY* 1.3 87.6 - - - +
318D ARG* 1.3 62.9 + - - +
320D LEU* 3.3 5.6 + - + +
321D LYS* 3.0 24.0 + - - +
340D SER* 3.6 27.5 - - - +
341D PHE* 5.8 0.3 - - - -
513D PRO* 3.9 33.2 - - + -
514D HIS* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ARG* 5.0 21.2 - - - +
314D ALA 5.3 0.9 + - - +
315D ASP* 2.7 52.6 + - - +
316D GLY 3.3 0.8 - - - -
317D PRO* 1.3 79.2 - - - +
319D LEU* 1.3 79.2 + - + +
321D LYS* 3.3 10.8 + - + +
322D GLU* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D ASP* 3.0 20.3 + - + +
316D GLY 3.9 2.2 - - - +
318D ARG* 1.3 95.6 - - - +
320D LEU* 1.3 67.5 + - - +
322D GLU* 3.5 23.1 - - - +
323D LEU* 2.9 22.5 + - - +
428D THR* 3.2 41.1 - - + +
429D THR* 5.4 0.4 - - - -
431D LEU* 4.4 13.7 - - + -
432D GLY* 3.7 19.3 - - - +
435D MET* 3.5 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 3.9 24.7 - - + -
306D VAL* 3.7 46.4 - - + -
310D ILE* 4.2 11.7 - - + -
316D GLY 2.9 17.2 + - - +
317D PRO 3.6 4.0 - - - +
319D LEU* 1.3 76.5 - - - +
321D LYS* 1.3 57.9 + - - +
323D LEU* 3.4 3.5 + - + +
324D SER* 2.9 29.5 + - - -
331D VAL* 4.5 5.4 - - + -
340D SER* 4.0 24.0 - - - +
341D PHE* 4.1 18.4 - - + -
373D VAL* 5.3 1.8 - - + -
431D LEU* 4.4 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ASN* 4.9 12.7 + - - -
317D PRO 3.0 17.1 + - - +
318D ARG* 3.5 9.0 - - + +
320D LEU* 1.3 75.9 - - - +
322D GLU* 1.3 59.5 + - - +
324D SER* 3.3 6.0 + - - -
325D ASP* 2.8 54.5 + - - +
341D PHE* 4.5 14.8 - - + -
342D ASP* 6.5 1.3 - - + -
345D ASP* 3.7 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ARG* 3.0 18.3 + - + +
319D LEU* 3.2 26.5 + - - +
321D LYS* 1.3 76.9 - - - +
323D LEU* 1.3 52.9 + - - +
325D ASP* 3.3 4.9 + - - +
326D ARG* 2.7 44.7 + - + +
435D MET* 3.3 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ILE* 5.0 5.6 - - + -
304D LEU* 4.1 29.6 - - + -
319D LEU 2.9 16.5 + - - +
320D LEU* 3.7 4.0 - - + +
322D GLU* 1.3 75.9 - - - +
324D SER* 1.3 65.7 + - - +
326D ARG* 4.3 0.9 - - + -
327D ALA* 3.0 23.9 + - - +
329D ILE* 4.5 13.6 - - + +
371D ILE* 5.2 2.2 - - + -
431D LEU* 4.0 27.1 - - + -
434D MET* 4.3 12.8 - - + -
435D MET* 3.7 18.7 - - + +
438D ILE* 4.0 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 4.3 7.4 - - - +
320D LEU 2.9 18.1 + - - -
321D LYS 3.3 4.9 + - - -
323D LEU* 1.3 78.2 - - - +
325D ASP* 1.3 59.0 + - - +
328D GLN* 2.9 10.0 + - - -
329D ILE* 2.7 50.4 + - - +
331D VAL* 3.4 19.0 - - - +
341D PHE* 3.9 13.7 - - - -
347D LYS* 3.6 13.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A HIS* 6.3 2.7 - - + -
321D LYS* 2.8 57.0 + - - +
322D GLU* 3.8 4.7 - - - +
324D SER* 1.3 71.7 + - - +
326D ARG* 1.3 68.3 + - - +
328D GLN* 3.1 21.2 + - - +
341D PHE* 6.0 0.5 - - - -
345D ASP* 4.2 3.8 - - - +
347D LYS* 2.6 34.4 + - - +
441D VAL 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 5.7 0.2 - - - +
322D GLU* 2.7 29.4 + - + +
323D LEU* 3.7 3.4 - - - +
325D ASP* 1.3 76.3 - - - +
327D ALA* 1.3 57.3 + - + +
328D GLN 3.8 0.2 + - - -
435D MET* 3.2 43.2 + - - +
436D SER* 4.0 13.4 + - - +
438D ILE* 2.7 37.0 + - + +
440D PRO* 3.4 31.8 - - + +
441D VAL* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ILE* 4.8 4.0 - - + -
323D LEU* 3.0 9.8 + - + +
326D ARG* 1.3 75.5 - - - +
328D GLN* 1.3 66.3 + - - +
329D ILE* 3.4 26.3 + - + +
438D ILE* 3.9 23.6 - - + -
439D PHE 4.5 0.4 - - - -
441D VAL* 3.6 14.4 - - + +
444D ARG* 2.8 36.3 + - - +
----------------------------------------------------------
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