Contacts of the helix formed by residues 296 - 310 (chain B) in PDB entry 1C7G
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 GLY 296 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP 3.8 8.7 - - - -
69B GLU* 2.7 21.6 + - - +
76B ASN* 3.0 40.2 - - - +
294B LEU 3.8 0.6 + - - -
295B ALA* 1.3 72.0 - - - +
297B ARG* 1.3 60.4 + - - +
299B MET* 3.1 22.1 + - - +
300B GLU 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 4.5 1.3 - - - -
64B MET* 3.5 46.8 - - - +
67B GLY* 3.7 12.9 - - - -
69B GLU* 3.2 15.2 + - - +
295B ALA* 3.8 11.7 - - + -
296B GLY* 1.3 75.6 - - - +
298B ASP* 1.3 69.1 + - - +
300B GLU* 3.4 7.1 + - - +
301B ALA* 3.0 26.9 + - - +
56D MET* 3.4 15.8 - - - +
61D TRP* 4.6 4.6 - - - -
64D MET* 3.3 27.9 - - - +
261D VAL* 6.0 1.8 - - - +
262D ASN* 2.9 35.4 + - - +
263D ILE* 4.2 11.3 - - - +
297D ARG* 5.0 1.0 - - - +
298D ASP* 2.7 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 4.1 5.7 - - - +
261B VAL* 5.1 0.7 - - - +
263B ILE* 3.7 26.1 - - + +
294B LEU* 4.3 14.2 - - + +
295B ALA* 3.1 31.6 + - - +
297B ARG* 1.3 83.6 + - - +
299B MET* 1.3 61.0 + - - +
300B GLU 3.2 0.4 - - - -
301B ALA* 3.8 6.2 - - - +
302B MET* 3.1 28.2 + - - +
263D ILE* 5.1 1.6 - - - +
297D ARG* 2.8 29.2 + - - -
298D ASP* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 4.6 6.5 - - - +
76B ASN* 4.1 12.3 - - + +
77B PHE* 4.0 33.7 - - + +
80B LEU* 3.9 17.8 - - + +
95B PRO* 4.3 6.5 - - - -
290B SER 3.6 17.9 - - - +
291B TYR* 3.8 30.1 - - + +
294B LEU* 4.0 22.7 - - + +
295B ALA 3.3 5.7 + - - +
296B GLY* 3.1 25.1 + - - +
298B ASP* 1.3 75.0 - - - +
300B GLU* 1.3 66.4 + - - +
302B MET* 3.6 6.0 + - - +
303B ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 3.7 32.0 - - - +
66B ILE* 4.3 10.3 - - + +
76B ASN* 2.9 29.0 + - - +
79B HIS* 2.5 43.1 + - - +
296B GLY 3.2 6.0 + - - +
297B ARG 3.5 9.6 - - - +
299B MET* 1.3 78.6 - - - +
301B ALA* 1.3 62.8 + - - +
303B ALA* 3.1 5.3 + - - +
304B ILE* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B MET* 4.2 19.1 - - - -
60B GLN* 3.1 18.1 + - - +
63B GLY 5.4 0.2 - - - -
64B MET* 4.2 22.0 - - + -
261B VAL* 3.8 7.0 - - + -
297B ARG 3.0 16.5 + - - +
298B ASP* 3.9 7.2 - - - +
299B MET 3.4 0.2 - - - -
300B GLU* 1.3 76.9 - - - +
302B MET* 1.3 56.8 + - - +
304B ILE* 3.3 9.5 + - - +
305B GLY 2.8 24.6 + - - -
297D ARG* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.7 28.4 - - + +
255B GLY* 4.1 12.6 - - - -
259B CYS* 4.1 18.4 - - + +
261B VAL* 3.6 15.2 - - + +
263B ILE 5.3 0.4 - - - +
264B GLY* 3.8 10.5 - - - -
265B GLY* 3.6 42.0 - - - +
266B PHE* 3.7 18.2 - - + -
294B LEU* 4.0 12.1 - - + -
298B ASP 3.1 17.7 + - - +
299B MET* 3.9 3.4 - - - +
301B ALA* 1.3 74.4 - - - +
303B ALA* 1.3 65.1 + - - +
306B LEU* 3.0 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 4.1 8.7 - - + -
80B LEU* 3.7 33.8 - - - +
83B THR* 3.7 26.9 + - - +
299B MET 3.0 17.9 + - - +
300B GLU* 3.5 6.3 - - - +
302B MET* 1.3 77.7 - - - +
304B ILE* 1.3 63.5 + - + +
306B LEU* 3.7 1.0 + - - +
307B ARG* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS* 3.6 26.9 - - + +
60B GLN* 3.5 28.5 - - + +
63B GLY* 4.2 6.1 - - - -
300B GLU* 3.0 40.9 + - + +
301B ALA* 3.7 5.6 - - - +
303B ALA* 1.3 77.0 - - + +
305B GLY* 1.3 65.0 + - - +
307B ARG* 3.1 10.6 + - + +
308B GLU* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.3 18.3 - - - +
259B CYS 3.3 22.2 - - - -
260B LEU* 3.8 5.5 - - - +
301B ALA 2.8 14.9 + - - -
302B MET 3.9 0.2 - - - -
304B ILE* 1.3 73.8 - - - +
306B LEU* 1.3 61.1 + - - +
308B GLU* 3.0 7.4 + - - +
309B ALA* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.5 1.6 - - + -
83B THR* 4.3 9.6 - - + -
84B VAL* 4.0 29.8 - - + -
87B LEU* 3.8 14.4 - - + -
88B PHE* 4.0 30.7 - - + -
219B VAL* 5.2 3.8 - - + -
253B MET* 4.8 2.7 - - + -
258B ASP 4.9 5.2 - - - +
259B CYS* 3.7 26.7 + - - +
266B PHE* 4.5 10.3 - - + -
302B MET* 3.0 17.9 + - + +
303B ALA 3.9 5.2 - - - +
304B ILE 3.3 0.2 - - - -
305B GLY* 1.3 75.3 - - - +
307B ARG* 1.3 63.8 + - - +
309B ALA* 3.5 7.9 + - - +
310B MET* 3.6 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 5.2 4.6 - - - +
83B THR* 3.2 41.9 + - - +
86B GLU* 2.6 44.6 + - - -
87B LEU* 4.2 16.6 - - + +
238B LYS* 5.9 0.6 - - - +
303B ALA 3.6 7.0 + - - +
304B ILE* 3.1 13.2 + - + +
305B GLY 3.1 0.6 - - - -
306B LEU* 1.3 77.9 - - - +
308B GLU* 1.3 66.5 + - + +
310B MET* 3.0 22.2 + - + +
311B GLN* 4.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.2 13.4 - - + +
57B SER* 2.4 30.9 + - - -
59B LYS* 4.0 7.1 - - - +
60B GLN* 3.5 10.3 - - - +
260B LEU* 4.0 8.5 - - + -
304B ILE* 3.0 27.5 + - + +
305B GLY 3.0 7.2 + - - +
307B ARG* 1.3 76.0 - - + +
309B ALA* 1.3 61.1 + - - +
310B MET 3.1 1.6 + - - -
311B GLN* 3.1 22.1 + - - +
314B TYR* 3.9 7.7 - - - +
410B ARG* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 3.3 33.4 - - + +
237B ILE* 4.5 0.5 - - - +
258B ASP 3.4 26.5 - - - +
260B LEU* 4.0 3.6 - - + +
305B GLY 2.9 13.0 + - - +
306B LEU* 3.7 8.3 - - + +
307B ARG 3.2 0.4 - - - -
308B GLU* 1.3 76.4 - - - +
310B MET* 1.3 59.5 + - - +
311B GLN 3.2 2.7 + - - +
314B TYR* 3.6 29.5 - - + -
315B ILE* 4.4 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.0 26.0 - - + -
88B PHE* 5.1 1.3 - - + -
219B VAL* 3.8 29.4 - - + -
237B ILE* 3.6 24.3 + - - +
238B LYS* 3.9 38.6 + - + +
241B VAL* 4.3 20.0 - - + -
306B LEU* 3.6 34.3 - - + +
307B ARG* 3.0 13.4 + - + +
309B ALA* 1.3 76.7 - - - +
311B GLN* 1.3 63.5 + - - +
312B TYR 3.3 3.3 + - - -
----------------------------------------------------------
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