Contacts of the helix formed by residues 236 - 252 (chain A) in PDB entry 1G3I
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ALA 5.1 1.0 + - - -
234A LEU* 2.7 14.0 + - + +
235A ILE* 1.3 83.9 - - - +
237A PRO* 1.3 60.5 - - - +
238A GLU* 3.1 13.3 + - - +
239A GLU* 2.6 74.3 + - - +
240A LEU 3.4 0.7 + - - -
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Residues in contact with PRO 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ARG* 6.3 0.4 - - - +
235A ILE* 3.1 20.3 - - + -
236A ASN* 1.3 87.1 - - - +
238A GLU* 1.3 58.1 + - - +
239A GLU 3.0 5.2 + - - -
240A LEU* 3.3 17.5 + - + +
241A LYS* 3.3 27.2 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ASN* 2.8 14.3 + - - +
237A PRO* 1.3 75.3 - - - +
239A GLU* 1.3 56.8 + - - +
241A LYS* 4.5 12.5 - - + +
242A GLN* 3.7 16.5 + - - +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 5.2 7.3 - - - +
234A LEU* 5.4 7.8 - - - +
235A ILE 4.3 3.4 - - - +
236A ASN* 2.6 49.6 + - + +
238A GLU* 1.3 73.3 - - - +
240A LEU* 1.3 67.4 + - - +
241A LYS 3.1 1.3 - - - -
242A GLN* 2.9 19.0 + - + -
243A LYS* 2.9 19.8 + - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET* 3.9 23.8 - - + -
111A VAL* 3.4 33.1 - - + +
112A ARG* 3.9 50.5 - - - +
115A GLU* 5.1 12.8 - - + +
235A ILE* 4.3 15.5 + - + +
236A ASN 3.4 2.8 + - - +
237A PRO* 3.3 14.8 + - + +
239A GLU* 1.3 76.0 - - - +
241A LYS* 1.3 65.8 + - + +
243A LYS* 2.8 17.9 + - - +
244A ALA* 3.0 10.6 + - - +
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A MET* 4.1 24.9 - - + -
237A PRO* 3.3 22.9 - - - +
238A GLU* 4.5 9.4 - - + +
240A LEU* 1.3 77.8 - - - +
242A GLN* 1.3 54.3 + - - +
243A LYS 2.7 11.1 + - - -
244A ALA* 2.8 14.8 + - - +
245A ILE* 3.0 17.9 + - - +
294A LYS 4.5 9.2 + - - -
295A HIS* 4.0 37.2 - - + +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU 3.7 14.3 + - - +
239A GLU* 2.9 17.8 + - + +
241A LYS* 1.3 74.4 - - - +
243A LYS* 1.3 50.0 + - - +
245A ILE* 4.3 22.5 - - - +
246A ASP* 2.5 35.6 + - - +
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.4 17.0 - - + +
114A GLN* 5.7 5.3 - - - +
115A GLU* 3.3 32.4 + - - +
239A GLU* 2.9 14.7 + - + +
240A LEU* 2.8 12.6 + - - +
241A LYS 2.7 0.2 + - - -
242A GLN* 1.3 77.4 - - - +
244A ALA* 1.3 61.6 + - - +
245A ILE 3.2 1.1 - - - -
246A ASP* 3.2 13.4 + - + +
247A ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 4.6 4.7 - - + +
107A ALA* 3.6 23.2 - - + +
108A MET* 3.7 28.9 - - + +
111A VAL* 4.0 8.0 - - + +
240A LEU 3.0 5.8 + - - +
241A LYS* 2.8 7.3 + - - +
243A LYS* 1.3 73.4 - - - +
245A ILE* 1.3 68.1 + - + +
247A ALA* 3.1 10.1 + - - +
248A VAL* 2.9 27.5 + - - +
295A HIS* 5.9 1.3 - - + -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A THR* 5.1 1.8 - - + -
241A LYS 3.0 16.7 + - - +
242A GLN* 4.5 20.6 - - - +
244A ALA* 1.3 77.9 - - - +
246A ASP* 1.3 57.8 + - - +
248A VAL* 3.3 3.0 + - - +
249A GLU* 2.8 48.8 + - - +
295A HIS* 3.2 34.5 - - + +
296A GLY* 3.8 15.0 - - - -
297A MET 3.4 24.2 - - - +
298A VAL* 3.8 18.2 - - + -
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Residues in contact with ASP 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLN* 2.5 32.3 - - - +
243A LYS* 3.2 16.6 + - + +
245A ILE* 1.3 79.6 - - - +
247A ALA* 1.3 55.7 - - - +
249A GLU* 2.9 11.3 + - - +
250A GLN* 2.4 51.2 + - + +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.7 22.0 - - + +
107A ALA* 4.2 3.4 - - + -
110A LEU* 5.9 1.6 - - + -
111A VAL* 4.4 11.4 - - + -
243A LYS 3.1 9.4 + - - +
244A ALA* 3.2 14.8 - - - +
246A ASP* 1.3 77.7 - - - +
248A VAL* 1.3 59.4 + - - +
250A GLN* 4.8 1.1 - - - -
251A ASN* 2.9 42.7 + - - +
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.4 5.6 - - + -
100A ILE* 4.8 1.8 - - + -
103A LEU* 3.6 19.1 - - + +
104A THR* 3.3 45.3 - - + +
107A ALA* 3.5 16.6 - - + -
244A ALA 2.9 10.6 + - - +
245A ILE* 3.6 7.0 - - - +
247A ALA* 1.3 75.9 - - - +
249A GLU* 1.3 66.7 + - - +
252A GLY* 3.0 16.3 + - - +
298A VAL* 4.4 14.6 - - + -
299A LYS 5.4 0.4 - - - +
303A ILE* 2.9 33.7 - - + +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 2.8 33.0 + - + +
246A ASP* 3.5 9.6 - - - +
248A VAL* 1.3 79.0 - - - +
250A GLN* 1.3 63.7 + - + +
297A MET 3.4 7.8 - - - +
298A VAL* 3.3 11.5 - - + -
299A LYS* 3.1 66.2 + - + +
302A HIS* 3.3 32.1 - - - +
303A ILE* 4.2 0.7 + - - -
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.3 24.4 + - - +
37A ARG* 3.1 41.3 + - - +
38A MET* 3.5 18.9 - - + +
45A ARG* 4.3 15.1 + - - -
46A HIS* 5.3 5.5 - - - -
246A ASP* 2.4 45.2 + - + +
247A ALA* 4.7 0.4 - - - +
249A GLU* 1.3 76.5 + - + +
251A ASN* 1.3 72.3 + - - +
252A GLY 3.8 0.7 - - - -
302A HIS* 4.3 4.6 - - - +
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Residues in contact with ASN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 6.1 1.6 - - + -
34A ARG* 2.8 27.6 + - + +
38A MET* 4.5 11.4 - - - +
74A ALA* 5.3 3.4 + - + +
75A ASN 4.6 9.1 + - - -
76A ALA* 3.0 30.3 - - + +
77A PRO* 3.3 8.9 - - - +
247A ALA* 2.9 29.0 + - - +
250A GLN* 1.3 86.5 - - - +
252A GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.3 6.1 + - - +
77A PRO* 3.5 10.5 - - - -
103A LEU* 4.3 7.9 - - - -
247A ALA 4.4 1.6 - - - -
248A VAL 3.0 18.6 + - - -
250A GLN 3.8 0.6 - - - -
251A ASN* 1.3 78.1 - - - +
253A ILE* 1.3 57.1 + - - -
303A ILE* 4.0 11.5 - - - +
304A LEU 2.7 32.7 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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