Contacts of the helix formed by residues 321 - 333 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 4.3 5.8 - - + +
319A LYS 4.7 1.1 - - - +
320A VAL* 1.3 80.2 - - - +
322A SER* 1.3 66.4 + - - +
323A GLU* 2.7 22.7 + - + +
324A GLN* 3.0 33.1 + - - +
325A LEU 3.2 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 5.1 10.8 - - - -
314A THR* 5.0 3.8 + - - -
318A GLU* 3.1 20.6 + - - -
320A VAL 3.0 4.2 + - - -
321A PRO* 1.3 69.1 - - - +
323A GLU* 1.3 50.5 + - - +
325A LEU* 2.6 19.1 + - - +
326A THR* 2.6 46.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO* 2.7 26.5 + - + +
322A SER* 1.3 77.9 - - - +
324A GLN* 1.3 78.0 + - - +
326A THR* 3.0 5.8 + - - -
327A LEU* 3.0 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.1 23.9 - - + +
321A PRO* 3.0 43.1 + - - +
323A GLU* 1.3 91.7 + - - +
325A LEU* 1.3 60.3 + - - +
327A LEU* 3.8 7.4 - - - +
328A LEU* 2.9 42.1 + - + +
331A GLU* 5.0 0.3 - - - +
379A ALA 4.6 3.5 - - - +
380A ALA* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 4.3 17.3 - - + -
290A LEU* 3.7 41.1 - - + +
312A VAL* 4.0 14.5 - - + +
314A THR* 3.5 32.3 - - + -
318A GLU* 4.4 12.3 - - + -
320A VAL* 3.7 15.9 - - + +
321A PRO 3.2 0.6 + - - -
322A SER* 2.6 26.9 + - - +
324A GLN* 1.3 79.5 - - - +
326A THR* 1.3 56.5 + - - +
328A LEU* 3.8 7.7 - - + +
329A VAL* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 5.1 8.9 - - + +
311A MET* 5.0 5.8 - - - -
312A VAL* 3.4 35.1 - - + +
322A SER* 2.6 36.8 + - - -
323A GLU* 3.6 5.0 + - - -
325A LEU* 1.3 72.2 - - - +
327A LEU* 1.3 64.5 + - - +
328A LEU 3.1 1.8 - - - -
329A VAL* 3.4 9.3 + - + +
330A ARG* 3.0 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 3.0 29.1 + - + +
324A GLN* 4.1 7.0 - - - +
326A THR* 1.3 78.0 - - - +
328A LEU* 1.3 58.6 + - - +
330A ARG* 2.6 44.2 + - - +
331A GLU* 2.8 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 6.4 0.2 - - + -
290A LEU* 4.2 14.6 - - + -
324A GLN* 2.9 26.9 + - + +
325A LEU* 3.8 10.5 - - + +
327A LEU* 1.3 79.0 - - - +
329A VAL* 1.3 55.4 + - + +
331A GLU* 3.0 17.2 + - - +
332A PHE* 2.8 41.5 + - + +
376A LEU* 3.3 46.9 - - + +
379A ALA* 3.3 39.5 - - + +
380A ALA* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 4.7 10.1 - - + -
285A ILE* 4.4 19.7 - - + -
296A ILE* 4.5 5.4 - - + -
310A ILE* 4.6 19.5 - - + -
312A VAL* 3.9 18.8 - - + -
325A LEU 3.1 19.5 - - - +
326A THR* 3.4 8.9 + - + +
328A LEU* 1.3 76.5 - - + +
330A ARG* 1.3 61.2 + - + +
331A GLU 3.1 0.3 + - - -
333A PHE* 3.0 51.1 + - + +
335A LEU* 4.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 4.9 20.0 - - + -
326A THR* 3.0 22.2 - - + +
327A LEU* 2.6 47.9 + - + +
329A VAL* 1.3 79.5 - - + +
331A GLU* 1.3 106.7 + - - +
333A PHE 3.6 13.9 - - - +
335A LEU* 5.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN 5.0 0.2 - - - +
327A LEU* 2.8 29.5 - - - +
328A LEU* 3.0 29.8 - - - +
329A VAL 2.9 0.2 - - - -
330A ARG* 1.3 102.2 + - - +
332A PHE* 1.3 65.7 + - + +
333A PHE 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 2.8 22.7 + - + +
331A GLU* 1.3 82.2 - - + +
333A PHE* 1.3 70.5 + - + +
372A LYS* 4.0 30.6 + - + -
375A LEU* 3.2 57.0 - - + -
376A LEU* 3.4 29.8 - - + -
379A ALA* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR* 3.7 32.8 - + - -
281A VAL* 3.6 35.2 - - + -
284A ASN* 4.5 2.5 - - + -
285A ILE* 5.5 1.3 - - + -
329A VAL* 3.0 31.7 + - + +
330A ARG* 3.6 19.9 - - - +
331A GLU 4.9 0.2 - - - +
332A PHE* 1.3 87.3 - - + +
334A ASP* 1.3 61.4 + - - +
335A LEU* 4.0 21.3 + - + +
343A MET* 4.3 7.9 - - - -
372A LYS* 3.7 27.6 - - + -
376A LEU* 3.6 35.0 - - + -
----------------------------------------------------------
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