Contacts of the helix formed by residues 321 - 333 (chain D) in PDB entry 1P7L
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 PRO 321 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D GLU* 4.3 5.2 - - + +
319D LYS 4.7 1.8 - - - +
320D VAL* 1.3 82.7 - - - +
322D SER* 1.3 68.5 + - - +
323D GLU* 2.7 23.0 + - + +
324D GLN* 3.0 28.3 + - - +
325D LEU 3.2 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D VAL* 5.1 11.0 - - - -
314D THR* 5.0 3.5 + - - -
318D GLU* 2.9 20.7 + - - -
320D VAL 3.0 4.5 + - - -
321D PRO* 1.3 69.8 - - - +
323D GLU* 1.3 50.3 + - - +
325D LEU* 2.6 19.4 + - - +
326D THR* 2.6 45.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D PRO* 2.7 26.4 + - + +
322D SER* 1.3 79.1 + - - +
324D GLN* 1.3 75.7 + - - +
326D THR* 3.0 6.6 + - - -
327D LEU* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D VAL* 3.0 36.7 - - + +
321D PRO* 3.0 28.7 + - - +
323D GLU* 1.3 91.3 + - - +
325D LEU* 1.3 61.7 + - - +
327D LEU* 3.8 7.8 - - - -
328D LEU* 2.9 42.6 + - + +
379D ALA 4.4 4.0 - - - +
380D ALA* 3.9 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ILE* 4.2 17.9 - - + -
290D LEU* 3.8 39.5 - - + +
294D CYS* 5.8 0.2 - - + -
312D VAL* 3.9 15.7 - - + +
314D THR* 3.5 32.1 - - + +
318D GLU* 4.3 12.6 - - + -
320D VAL* 3.7 16.8 - - + +
321D PRO 3.2 0.8 + - - -
322D SER* 2.6 26.3 + - - +
324D GLN* 1.3 77.9 - - - +
326D THR* 1.3 55.1 + - - +
328D LEU* 3.9 7.6 - - + +
329D VAL* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 5.3 8.6 - - + +
311D MET* 5.1 5.2 - - - -
312D VAL* 3.5 34.4 - - + +
322D SER* 2.6 35.9 + - - -
323D GLU* 3.6 5.0 + - - -
325D LEU* 1.3 73.6 - - - +
327D LEU* 1.3 64.4 + - - +
328D LEU 3.1 1.9 + - - -
329D VAL* 3.5 8.4 + - + +
330D ARG* 3.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D GLU* 3.0 29.0 + - + +
324D GLN* 4.1 7.0 - - - +
326D THR* 1.3 78.7 - - - +
328D LEU* 1.3 54.0 + - - +
330D ARG* 2.5 42.7 + - - +
331D GLU* 2.7 33.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D ILE* 6.4 0.7 - - + -
290D LEU* 4.2 13.5 - - + -
324D GLN* 2.9 24.7 + - + +
325D LEU* 3.9 10.1 - - + +
326D THR 3.1 0.2 - - - -
327D LEU* 1.3 78.4 - - - +
329D VAL* 1.3 55.7 + - - +
331D GLU* 2.9 16.5 + - - +
332D PHE* 2.8 41.2 + - + +
376D LEU* 3.3 48.0 - - + +
379D ALA* 3.2 41.3 - - + +
380D ALA* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D VAL* 4.7 6.3 - - + -
285D ILE* 4.3 20.2 - - + -
296D ILE* 4.5 10.1 - - + -
310D ILE* 4.6 19.7 - - + -
312D VAL* 3.9 19.5 - - + -
325D LEU 3.1 18.8 - - - +
326D THR* 3.6 8.1 - - + +
328D LEU* 1.3 77.6 - - + +
330D ARG* 1.3 62.4 + - + +
331D GLU 3.0 4.3 + - - -
333D PHE* 3.0 46.9 + - + +
335D LEU* 4.7 12.8 - - + -
376D LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 5.0 19.1 - - + -
326D THR* 3.0 21.1 - - + +
327D LEU* 2.5 48.3 + - + +
329D VAL* 1.3 78.0 - - + +
331D GLU* 1.3 107.7 + - - +
333D PHE 3.7 14.0 - - - +
335D LEU* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D GLN 5.1 0.2 - - - +
327D LEU* 2.7 31.3 - - - +
328D LEU* 2.9 28.5 + - + +
330D ARG* 1.3 101.9 + - - +
332D PHE* 1.3 65.9 + - + +
333D PHE 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LEU* 2.8 22.2 + - + +
331D GLU* 1.3 81.6 - - + +
333D PHE* 1.3 70.5 + - + +
334D ASP 4.3 0.2 + - - -
372D LYS* 3.9 32.2 + - - +
375D LEU* 3.1 58.6 - - + -
376D LEU* 3.4 27.8 - - + -
379D ALA* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D TYR* 3.7 31.0 - + - -
281D VAL* 3.6 35.9 - - + -
284D ASN* 4.5 2.2 - - + -
285D ILE* 5.5 1.1 - - + -
329D VAL* 3.0 30.6 + - + +
330D ARG* 3.7 19.4 - - - +
331D GLU 5.0 0.2 - - - +
332D PHE* 1.3 86.5 - - + +
334D ASP* 1.3 59.8 + - - +
335D LEU* 3.9 22.1 + - + +
343D MET* 4.3 8.5 - - - -
372D LYS* 3.6 29.2 - - + -
376D LEU* 3.5 35.9 - - + -
----------------------------------------------------------
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