Contacts of the helix formed by residues 319 - 334 (chain A) in PDB entry 4R0C
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 ASN 319 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 3.3 26.4 - - - +
318A ARG* 1.3 83.3 - - - +
320A SER* 1.3 62.4 + - - +
321A GLY* 2.9 8.1 + - - +
322A ALA* 2.6 47.4 + - - +
323A VAL 4.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 4.1 14.4 + - - +
319A ASN* 1.3 72.7 - - - +
321A GLY* 1.3 61.6 + - - +
322A ALA 3.0 5.8 + - - -
323A VAL* 3.2 23.4 + - - +
324A ILE* 3.6 7.4 + - - +
806A LMT 3.8 28.7 + - - +
23B LEU* 3.9 21.0 - - - +
27B TRP* 5.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ASN* 2.9 10.1 + - - +
320A SER* 1.3 78.0 - - - +
322A ALA* 1.3 56.7 + - - +
323A VAL 3.4 0.2 - - - -
324A ILE* 3.3 16.4 - - - +
325A THR* 2.9 27.9 + - - -
20B HIS* 4.5 13.0 - - - -
23B LEU* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLN 5.4 0.4 - - - +
317A PHE* 3.9 25.2 - - + -
318A ARG* 3.9 10.8 - - + +
319A ASN* 2.6 27.7 + - - +
320A SER 3.0 0.2 - - - -
321A GLY* 1.3 72.4 - - - +
323A VAL* 1.3 59.8 + - - +
325A THR* 2.9 13.2 + - - -
326A ALA* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 3.9 25.8 - - + -
308A ALA* 4.4 6.1 - - + -
312A ARG* 4.1 24.2 - - + -
317A PHE* 4.0 21.5 - - + -
319A ASN 4.3 0.2 - - - +
320A SER* 3.2 13.2 + - - +
322A ALA* 1.3 75.1 - - - +
324A ILE* 1.3 61.9 + - + +
326A ALA* 3.2 21.2 + - - +
327A MET* 3.2 12.9 + - + +
806A LMT 3.7 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER 3.9 4.7 - - - +
321A GLY* 3.3 15.2 + - - +
322A ALA 3.1 0.6 - - - -
323A VAL* 1.3 77.4 - - - +
325A THR* 1.3 62.3 + - - +
327A MET* 2.9 39.6 + - + +
328A GLU* 3.0 19.1 + - - +
806A LMT 5.1 7.2 - - + -
20B HIS* 3.5 29.8 - - + +
22B THR* 4.1 19.1 - - + +
23B LEU* 3.9 39.0 - - + -
26B VAL* 4.3 13.9 - - + -
339B VAL* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLY 2.9 15.2 + - - -
322A ALA* 2.9 13.7 + - - -
324A ILE* 1.3 75.5 - - - +
326A ALA* 1.3 57.8 + - - +
328A GLU* 3.2 15.8 + - + +
329A VAL* 2.8 40.8 + - + +
20B HIS* 5.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 5.3 0.2 - - - -
95A VAL* 4.1 12.6 - - + -
98A GLN* 3.9 16.1 - - + +
317A PHE* 3.7 35.7 - - + -
322A ALA 2.8 6.4 + - - +
323A VAL 3.2 10.8 - - - +
324A ILE 3.1 0.2 - - - -
325A THR* 1.3 76.3 - - - +
327A MET* 1.3 58.5 + - - +
329A VAL* 3.4 7.2 + - - +
330A THR* 3.0 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.9 31.0 - - + +
95A VAL* 3.5 20.4 - - + -
323A VAL* 3.5 10.5 - - + +
324A ILE* 2.9 34.3 + - + +
326A ALA* 1.3 74.8 - - - +
328A GLU* 1.3 60.2 + - - +
330A THR* 3.3 7.6 + - - -
331A MET* 2.9 33.3 + - - +
806A LMT 4.5 15.7 - - + -
26B VAL* 5.2 0.2 - - + -
339B VAL* 3.4 34.5 - - + -
343B PHE* 3.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 3.0 20.6 + - + +
325A THR* 3.2 16.8 + - + +
327A MET* 1.3 74.0 - - - +
329A VAL* 1.3 60.6 + - + +
331A MET 3.2 0.9 + - - -
332A ALA* 2.8 26.4 + - - +
20B HIS* 2.9 34.3 + - - -
22B THR* 4.8 0.7 + - - -
335B ALA* 3.2 17.5 - - + +
336B GLY* 3.7 30.8 + - - +
339B VAL* 4.2 15.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
98A GLN* 3.8 28.9 - - + +
325A THR* 2.8 35.1 + - + +
326A ALA* 3.6 6.5 - - - +
328A GLU* 1.3 71.3 - - - +
330A THR* 1.3 64.5 + - - +
332A ALA* 3.1 9.3 + - + +
333A SER* 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 3.3 53.8 - - + +
91A LEU* 5.5 0.2 - - - -
94A GLY* 3.1 20.3 - - - -
98A GLN* 3.6 8.8 + - - -
326A ALA 3.0 18.0 + - - -
327A MET* 3.6 7.0 - - - -
329A VAL* 1.3 75.8 - - - +
331A MET* 1.3 67.0 + - + +
333A SER* 2.6 28.0 + - - +
334A MET* 3.2 7.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.3 43.1 - - - +
90A MET* 3.9 17.0 - - + -
91A LEU* 3.5 18.4 - - + +
327A MET 2.9 20.1 + - - +
328A GLU 3.6 4.0 - - - +
330A THR* 1.3 77.4 - - + +
332A ALA* 1.3 65.0 + - - +
334A MET* 2.9 26.4 + - + +
335A ALA* 3.7 2.9 + - - -
338A LEU* 4.7 5.5 - - - +
77B PHE* 5.8 3.4 - - - -
331B MET 5.3 1.6 - - - +
332B ALA* 5.3 1.2 - - - -
335B ALA* 4.1 17.5 - - + +
338B LEU* 4.3 26.8 - - + +
339B VAL* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU 2.8 13.6 + - - +
329A VAL* 3.1 14.6 + - + +
331A MET* 1.3 77.3 - - - +
333A SER* 1.3 62.2 + - - +
335A ALA* 3.2 22.9 + - - +
332B ALA* 3.7 23.3 - - + +
335B ALA* 3.8 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 5.8 0.7 - - - +
133A VAL* 6.2 0.2 - - - +
329A VAL* 3.0 12.7 + - - -
330A THR* 2.6 25.7 + - - +
332A ALA* 1.3 71.8 - - - +
334A MET* 1.3 62.0 + - - +
335A ALA* 3.0 10.2 + - - +
336A GLY 4.2 4.5 + - - -
337A TYR 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.9 15.9 - - + -
87A LEU* 4.2 16.4 - - + -
90A MET* 3.6 27.4 - - + +
330A THR 3.4 14.4 - - - +
331A MET* 2.9 32.2 + - + +
333A SER* 1.3 83.4 + - - +
335A ALA* 1.3 64.6 + - - +
336A GLY 3.3 0.9 - - - -
337A TYR* 3.1 48.9 + - + +
338A LEU* 2.9 25.8 + - + +
----------------------------------------------------------
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