Contacts of the helix formed by residues 322 - 338 (chain A) in PDB entry 5I73
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 GLU 322 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLN 4.4 6.5 - - - +
319A LYS* 3.1 44.7 + - - +
321A LEU* 1.3 78.4 - - + +
323A THR* 1.3 59.9 + - - +
324A GLY* 3.0 12.0 + - - +
325A VAL* 3.5 17.2 + - + +
326A TRP* 3.5 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 3.6 3.9 + - - -
322A GLU* 1.3 70.7 - - - +
324A GLY* 1.3 58.5 + - - +
325A VAL 3.7 0.2 - - - -
326A TRP* 4.2 11.1 + - - +
327A ILE* 3.3 27.2 + - + +
551A PHE* 4.1 17.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 3.0 6.6 - - - +
323A THR* 1.3 80.5 - - - +
325A VAL* 1.3 61.2 + - - +
326A TRP 3.1 2.5 - - - -
327A ILE* 3.0 12.1 + - - +
328A ASP* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.5 37.7 - - + +
117A PHE* 3.9 8.4 - - + -
120A PRO* 5.3 2.2 - - + -
319A LYS* 3.2 38.6 - - + +
320A LEU* 4.2 11.0 - - + -
322A GLU* 3.5 22.4 - - - +
324A GLY* 1.3 75.9 - - - +
326A TRP* 1.3 69.7 + - + +
328A ASP* 3.5 10.9 - - - +
329A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.0 13.0 - - + -
120A PRO* 3.5 34.3 - - + -
123A ILE* 3.9 35.0 - - + -
124A MET* 3.6 32.4 - - + +
320A LEU* 3.1 33.6 + - + +
322A GLU 3.5 20.0 - - - -
323A THR* 4.4 9.9 - - - +
324A GLY 3.1 0.4 - - - -
325A VAL* 1.3 81.7 - - + +
327A ILE* 1.3 61.0 + - + +
329A ALA* 3.4 6.0 + - - +
330A ALA* 2.9 28.9 + - - +
551A PHE* 5.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 5.6 0.2 - - - -
323A THR* 3.3 25.8 - - + +
324A GLY* 3.0 9.6 + - - +
326A TRP* 1.3 73.0 - - - +
328A ASP* 1.3 64.5 + - - +
330A ALA* 3.3 6.3 + - - +
331A ALA* 2.9 30.0 + - + +
551A PHE* 4.1 35.0 - - + -
552A ILE* 4.4 18.8 - - + +
555A SER* 3.2 41.7 - - - +
705A 68P 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ILE* 3.7 23.3 - - + +
111A GLN* 5.2 2.9 + - - -
112A ASN* 3.4 20.9 + - - +
117A PHE* 5.0 0.4 - - + -
324A GLY* 2.8 18.7 + - - +
325A VAL* 3.5 11.7 - - - +
327A ILE* 1.3 80.3 - - - +
329A ALA* 1.3 56.8 + - - +
331A ALA* 3.9 4.6 - - - +
332A GLN* 2.9 30.5 + - - +
705A 68P 5.1 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.7 26.6 - - + -
120A PRO* 3.9 26.7 - - + +
121A TYR* 4.0 11.4 - - - -
124A MET* 4.3 1.3 - - - +
325A VAL 2.9 17.0 + - - +
326A TRP 3.7 5.2 - - - +
327A ILE 3.3 0.2 - - - -
328A ASP* 1.3 73.0 - - - +
330A ALA* 1.3 61.5 + - - +
332A GLN* 3.3 3.4 + - - +
333A ILE* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 3.8 19.2 - - + +
326A TRP 2.9 18.5 + - - +
327A ILE* 3.3 7.6 + - - +
329A ALA* 1.3 77.2 - - - +
331A ALA* 1.3 57.5 + - - +
333A ILE* 3.1 4.2 - - - +
334A PHE* 2.9 30.7 + - - +
548A PHE* 3.5 25.2 - - + +
551A PHE* 6.3 2.2 - - + -
552A ILE* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 2.9 17.2 + - + +
328A ASP* 3.9 5.2 - - - +
330A ALA* 1.3 75.8 - - - +
332A GLN* 1.3 58.8 + - - +
334A PHE* 3.7 1.7 - - - +
335A PHE* 2.9 38.9 + - + +
552A ILE* 3.5 28.8 - - + +
705A 68P 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 4.3 4.2 + - - -
101A ASN* 5.6 0.8 - - - +
104A ARG* 4.0 11.6 - - - +
105A PHE* 3.8 29.8 - - + +
108A ILE* 4.2 26.7 - - + +
117A PHE* 5.2 0.9 - - + -
121A TYR* 4.0 19.9 + - + +
328A ASP 2.9 20.0 + - - +
329A ALA* 3.4 8.7 - - - +
330A ALA 3.2 0.2 - - - -
331A ALA* 1.3 78.4 - - - +
333A ILE* 1.3 58.2 + - - +
336A SER* 2.8 34.2 + - - -
372A SER* 5.9 0.2 + - - -
705A 68P 3.1 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.6 36.6 - - + +
124A MET* 3.6 27.8 - - + +
125A ALA* 3.6 26.5 - - + -
129A GLY* 4.7 1.8 - - - -
329A ALA 2.9 15.7 + - - +
330A ALA* 3.1 16.8 - - - +
332A GLN* 1.3 73.0 - - - +
334A PHE* 1.3 61.0 + - - +
336A SER* 4.3 1.8 - - - +
337A LEU* 2.9 48.0 + - + +
368A ASN* 4.9 2.5 - - - +
369A CYS* 3.9 18.6 - - - -
548A PHE* 3.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY* 5.6 4.3 - - - -
132A LEU* 4.4 7.6 - - + -
330A ALA 2.9 18.0 + - - +
331A ALA* 3.7 4.3 - - - +
333A ILE* 1.3 80.0 - - - +
335A PHE* 1.3 79.2 + + - +
337A LEU* 3.5 1.3 + - - -
338A GLY* 2.8 29.0 + - - -
339A PRO* 3.6 33.5 - - + +
501A VAL* 4.4 11.9 - - + -
502A LEU* 3.5 35.9 - - + -
505A ALA* 3.8 26.7 - - + -
548A PHE* 4.1 11.0 - + + -
549A LEU* 3.5 28.3 - - + -
552A ILE* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 2.9 30.0 + - + +
334A PHE* 1.3 91.9 - + - +
336A SER* 1.3 66.4 + - - +
338A GLY* 3.5 7.5 + - - +
498A GLY* 3.7 27.1 - - - -
501A VAL* 5.3 0.7 - - + -
502A LEU* 3.8 22.7 - - + -
701A 68P 3.1 58.2 - + - -
705A 68P 3.4 59.5 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.5 8.7 - - - +
98A ASP* 6.0 0.2 - - - -
101A ASN* 3.4 8.4 + - - -
121A TYR* 4.9 5.8 - - - -
332A GLN* 2.8 24.2 + - - -
333A ILE* 3.3 6.9 + - - -
335A PHE* 1.3 79.5 - - - +
337A LEU* 1.3 61.1 + - - +
368A ASN* 2.4 32.1 + - - +
372A SER* 5.5 0.2 - - - -
701A 68P 3.7 3.3 - - - -
705A 68P 4.1 6.8 + - - -
707A NA 2.2 43.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.7 14.4 - - - -
96A ALA* 4.8 4.6 - - + +
129A GLY* 3.5 40.8 - - - +
130A ILE* 4.0 13.9 - - + +
133A PHE* 3.9 24.5 - - + -
333A ILE* 2.9 31.5 + - + +
334A PHE* 5.1 0.2 - - - -
336A SER* 1.3 76.3 - - - +
338A GLY* 1.3 64.4 + - - +
339A PRO* 2.7 16.4 - - + +
365A SER* 4.1 26.2 - - - +
368A ASN* 3.6 25.4 - - + +
369A CYS* 4.8 0.9 - - - -
701A 68P 4.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 2.4 28.0 + - - -
334A PHE* 2.8 16.8 + - - -
335A PHE* 3.9 2.5 - - - -
336A SER 3.4 1.6 - - - -
337A LEU* 1.3 71.6 - - - +
339A PRO* 1.3 73.3 - - - +
341A PHE* 4.3 6.1 - - - +
343A VAL* 5.4 0.3 - - - +
344A LEU* 4.5 3.0 - - - +
701A 68P 3.6 25.1 - - - -
----------------------------------------------------------
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