Contacts of the helix formed by residues 296 - 310 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP 3.8 9.6 - - - -
69A GLU* 2.9 18.0 + - - +
76A ASN* 3.0 39.3 - - - +
294A LEU 3.7 1.8 + - - -
295A ALA* 1.3 69.9 - - - +
297A ARG* 1.3 62.0 + - - +
299A MET* 3.1 25.5 + - - +
300A GLU 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 4.4 2.7 - - - +
64A MET* 3.7 44.4 - - - +
67A GLY* 3.9 13.2 - - - -
69A GLU* 3.2 15.9 + - - +
76A ASN* 3.8 1.0 + - - -
295A ALA* 3.8 9.8 - - + +
296A GLY* 1.3 76.7 - - - +
298A ASP* 1.3 68.1 + - - +
300A GLU* 3.3 7.5 + - - +
301A ALA* 3.0 26.2 + - - +
56C MET* 3.8 12.7 - - - +
61C TRP* 4.5 6.3 - - - -
64C MET* 3.4 32.5 - - - +
261C VAL* 6.2 1.0 - - - +
262C ASN* 2.9 35.8 + - - +
263C ILE* 4.4 8.9 - - - +
297C ARG* 5.0 0.4 - - - +
298C ASP* 2.7 29.9 + - - -
301C ALA* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 3.9 6.4 - - - +
261A VAL* 5.0 1.6 - - - +
263A ILE* 3.9 23.1 - - + +
294A LEU* 4.2 18.1 - - + +
295A ALA* 3.0 28.1 + - - +
297A ARG* 1.3 83.5 + - - +
299A MET* 1.3 65.3 + - - +
300A GLU 3.2 0.4 - - - -
301A ALA* 3.8 5.7 - - - +
302A MET* 3.1 25.3 + - - +
263C ILE* 5.0 1.7 - - - +
297C ARG* 2.7 31.6 + - - -
298C ASP* 4.0 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 6.1 0.2 - - - +
74A SER* 4.6 7.0 - - - +
76A ASN 4.0 12.6 - - - +
77A PHE* 4.0 32.3 - - + +
80A LEU* 3.8 24.0 - - + +
95A PRO* 4.6 2.9 - - - -
290A SER 3.8 13.9 - - - +
291A TYR* 3.8 30.5 - - + +
294A LEU* 4.1 20.0 - - + +
295A ALA 3.3 4.5 + - - +
296A GLY* 3.1 27.5 + - - +
298A ASP* 1.3 77.5 - - - +
300A GLU* 1.3 60.0 + - - +
302A MET* 3.6 6.4 + - - +
303A ALA* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 3.8 31.8 - - - +
66A ILE* 4.5 10.4 - - + +
76A ASN* 2.7 34.4 + - - +
79A HIS* 2.6 41.2 + - - +
296A GLY 3.3 3.1 + - - +
297A ARG 3.5 9.4 - - - +
298A ASP 3.2 0.6 - - - -
299A MET* 1.3 78.4 - - - +
301A ALA* 1.3 65.5 + - - +
303A ALA* 3.3 4.3 + - - +
304A ILE* 3.1 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 4.1 25.4 - - - -
60A GLN* 3.1 19.3 + - + +
63A GLY 5.4 0.2 - - - -
64A MET* 4.1 17.3 - - + -
261A VAL* 3.7 6.5 - - + -
297A ARG 3.0 15.0 + - - +
298A ASP* 3.9 7.4 - - - +
299A MET 3.4 0.2 - - - -
300A GLU* 1.3 77.5 - - - +
302A MET* 1.3 57.2 + - - +
304A ILE* 3.5 8.5 + - - +
305A GLY 3.0 22.3 + - - -
297C ARG* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.8 29.3 - - + +
255A GLY* 4.0 14.6 - - - -
259A CYS* 4.0 18.4 - - + +
261A VAL* 3.6 14.8 - - + +
263A ILE 5.3 0.4 - - - +
264A GLY* 3.8 9.0 - - - -
265A GLY 3.7 27.8 - - - +
266A PHE* 4.1 13.9 - - + -
294A LEU* 3.6 30.5 - - + -
298A ASP 3.1 15.9 + - - +
299A MET* 3.9 2.9 - - - +
301A ALA* 1.3 75.6 - - - +
303A ALA* 1.3 63.6 + - - +
304A ILE 3.2 0.2 - - - -
305A GLY 4.4 0.2 - - - +
306A LEU* 3.1 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.9 9.0 - - + +
80A LEU* 3.7 33.6 - - - +
83A THR* 3.6 29.7 + - - +
299A MET 3.1 18.3 + - - +
300A GLU* 3.8 4.7 - - - +
302A MET* 1.3 78.4 - - - +
304A ILE* 1.3 64.7 + - + +
306A LEU* 3.7 1.1 + - - -
307A ARG* 3.5 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 3.6 26.7 - - + +
60A GLN* 3.6 27.4 - - + +
63A GLY* 4.2 4.7 - - - -
300A GLU* 3.1 43.3 + - + +
301A ALA 3.7 4.0 - - - +
303A ALA* 1.3 77.0 - - + +
305A GLY* 1.3 60.8 + - - +
307A ARG* 3.1 10.7 + - + +
308A GLU* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.5 18.4 - - - +
259A CYS 3.4 22.0 - - - -
260A LEU* 3.5 6.8 - - - +
301A ALA 3.0 10.9 + - - -
302A MET 3.5 0.2 + - - -
304A ILE* 1.3 73.5 - - - +
306A LEU* 1.3 59.9 + - - +
308A GLU* 3.1 6.8 + - - -
309A ALA* 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 5.5 1.8 - - + -
83A THR* 4.2 11.4 - - + -
84A VAL* 3.7 31.6 - - + -
87A LEU* 3.9 13.0 - - + -
88A PHE* 4.0 32.1 - - + -
219A VAL* 5.3 2.5 - - + -
253A MET* 4.7 2.5 - - + -
258A ASP 4.9 3.4 - - - +
259A CYS* 3.6 32.6 + - - +
266A PHE* 4.5 2.2 - - + -
302A MET 3.1 18.6 + - - +
303A ALA 3.9 5.6 - - - +
304A ILE 3.2 0.2 - - - -
305A GLY* 1.3 76.2 - - - +
307A ARG* 1.3 62.0 + - - +
309A ALA* 3.4 13.0 + - + +
310A MET* 3.4 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 4.7 4.2 - - - +
83A THR* 3.4 39.4 + - - +
86A GLU* 2.8 41.6 + - - +
87A LEU* 4.3 19.7 - - + +
238A LYS* 5.3 3.8 - - - +
303A ALA 3.5 7.6 + - - +
304A ILE* 3.1 12.2 + - + +
306A LEU* 1.3 78.6 - - - +
308A GLU* 1.3 64.1 + - + +
310A MET* 3.3 19.0 + - + +
311A GLN* 4.3 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 2.4 29.5 + - - -
59A LYS* 3.9 7.3 - - - +
60A GLN* 3.6 7.4 - - - +
260A LEU* 4.0 7.7 - - + +
304A ILE* 2.9 31.6 + - + +
305A GLY 3.1 6.5 + - - +
307A ARG* 1.3 77.2 - - + +
309A ALA* 1.3 62.4 + - - +
310A MET 3.3 0.5 + - - -
311A GLN* 3.3 21.5 + - - +
314A TYR* 3.8 9.4 - - - +
410A ARG* 2.8 35.4 + - - +
15B THR* 4.0 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 3.3 33.4 - - + +
237A ILE* 4.6 0.2 - - - +
258A ASP* 3.3 26.0 - - - +
260A LEU* 3.8 5.6 - - + +
305A GLY 2.8 13.4 + - - +
306A LEU* 3.5 9.0 - - - +
307A ARG 3.2 0.2 - - - -
308A GLU* 1.3 78.4 - - - +
310A MET* 1.3 59.2 + - - +
311A GLN 3.2 3.8 + - - +
314A TYR* 3.5 24.4 - - + -
315A ILE* 4.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 4.0 20.4 - - + -
88A PHE* 4.8 2.7 - - + -
219A VAL* 4.0 27.8 - - + -
237A ILE* 3.6 22.2 + - + +
238A LYS* 4.0 41.1 + - + +
241A VAL* 4.3 26.7 - - + -
306A LEU* 3.4 35.9 - - + +
307A ARG* 3.5 11.4 - - + +
308A GLU 3.1 1.2 - - - -
309A ALA* 1.3 75.8 - - - +
311A GLN* 1.3 62.1 + - - +
312A TYR 3.3 3.5 + - - -
----------------------------------------------------------
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