Contacts of the helix formed by residues 238 - 257 (chain A) in PDB entry 6JKG
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 THR 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A HIS* 5.3 2.6 - - - -
236A ASP 4.8 3.4 - - - +
237A PHE* 1.3 74.3 - - - +
239A PHE* 1.3 63.1 + - - +
240A VAL* 3.5 10.7 + - - +
241A GLU* 2.9 40.7 + - - +
242A ASN* 2.6 29.6 + - - +
271A HIS* 5.0 1.3 - - - -
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A THR* 1.3 73.8 - - - +
240A VAL* 1.3 66.6 - - + +
242A ASN* 3.1 9.8 + - - +
243A VAL* 2.9 30.7 + - + +
269A GLU* 5.7 6.3 - - + -
270A HIS* 6.1 3.4 - + - -
271A HIS* 4.3 27.6 + + - -
242B ASN* 6.3 1.1 - - - -
269B GLU* 5.2 12.8 - - + -
271B HIS 3.2 31.2 - - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.5 34.8 - - + -
49A LEU* 4.3 21.3 - - + +
52A HIS* 3.7 34.3 - - + +
238A THR* 3.3 9.6 - - - +
239A PHE* 1.3 77.7 - - + +
241A GLU* 1.3 58.7 + - - +
243A VAL* 3.3 8.5 + - + +
244A VAL* 2.9 30.1 + - - +
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 4.4 21.4 + - + +
56A GLN* 3.3 24.6 + - - +
236A ASP 4.4 1.0 - - - +
237A PHE* 3.0 37.4 - - + -
238A THR* 2.9 42.9 + - - +
240A VAL* 1.3 75.4 - - - +
242A ASN* 1.3 57.5 + - - +
244A VAL* 3.4 1.2 + - - -
245A HIS* 2.9 22.9 + - - +
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Residues in contact with ASN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.2 22.9 + - - +
237A PHE* 3.2 29.6 - - - +
238A THR 2.6 21.9 + - - +
239A PHE* 3.1 8.2 + - - +
241A GLU* 1.3 73.8 - - - +
243A VAL* 1.3 54.5 + - + +
245A HIS* 2.8 9.3 + - - +
246A GLY* 2.7 33.1 + - - -
267A ILE* 6.1 4.3 - - + -
270A HIS* 3.1 40.5 + - + -
271A HIS* 4.1 2.6 - - - -
214B ILE* 5.3 6.8 - - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.1 15.7 - - + -
198A ILE* 5.7 0.5 - - - +
200A PRO* 4.2 14.6 - - + -
203A ILE 5.4 1.8 - - - +
239A PHE* 2.9 24.1 + - + +
240A VAL* 3.7 10.3 - - - +
242A ASN* 1.3 75.6 - - + +
244A VAL* 1.3 59.7 + - - +
246A GLY* 3.3 7.7 + - - +
247A HIS* 2.7 42.3 + - + -
267A ILE* 3.9 35.6 - - + +
269B GLU* 5.4 6.3 - - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.0 14.1 - - + -
52A HIS* 3.8 9.6 - - + +
53A MET* 3.5 42.8 - - + +
56A GLN* 3.2 40.8 - - + +
240A VAL 2.9 16.3 + - - +
241A GLU* 3.6 6.5 - - - +
243A VAL* 1.3 69.6 - - - +
245A HIS* 1.3 65.2 + - - +
246A GLY 3.0 5.6 + - - -
247A HIS* 3.1 16.2 + - - +
248A ILE* 3.1 21.4 + - + +
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Residues in contact with HIS 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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56A GLN* 3.3 19.8 + - - +
60A ARG* 4.1 24.2 + - - -
229A GLY* 5.4 0.8 - - - -
230A ASN 5.4 1.8 + - - -
233A ASN* 4.8 10.1 + - - -
234A LEU* 3.6 30.6 - - + +
237A PHE* 4.1 15.1 - + + -
241A GLU 2.9 10.5 + - - +
242A ASN* 2.8 17.3 + - - +
244A VAL* 1.3 72.4 - - - +
246A GLY* 1.3 59.9 + - - +
248A ILE* 4.1 7.3 - - - +
249A LEU* 3.2 58.0 + - + +
214B ILE* 4.5 4.5 - - + -
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Residues in contact with GLY 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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198A ILE* 5.5 0.9 - - - -
242A ASN 2.7 15.5 + - - -
243A VAL* 3.7 5.8 - - - -
244A VAL 3.0 1.0 - - - -
245A HIS* 1.3 71.7 - - - +
247A HIS* 1.3 66.1 + - - +
248A ILE 3.3 0.2 + - - -
249A LEU* 3.4 3.5 + - - +
250A ALA* 3.0 22.9 + - - +
267A ILE* 6.4 2.5 - - - -
214B ILE* 4.6 10.1 - - - +
215B LEU* 3.6 28.9 - - - +
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Residues in contact with HIS 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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49A LEU* 4.4 8.7 - - + -
53A MET* 4.1 14.4 - - + -
102A PHE* 3.7 18.8 - + + -
141A ILE* 3.7 18.8 - - + +
143A THR* 2.5 43.8 - - + +
198A ILE* 3.8 27.2 - - + +
200A PRO* 5.2 3.5 - - + +
243A VAL* 2.7 45.3 + - + -
244A VAL* 3.1 8.3 + - - +
246A GLY* 1.3 73.0 - - - +
248A ILE* 1.3 64.1 + - - +
250A ALA* 3.2 9.5 - - - +
251A ALA* 2.9 22.2 + - - +
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Residues in contact with ILE 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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53A MET* 5.8 1.3 - - - -
56A GLN* 4.1 13.2 - - + +
57A LEU* 3.6 40.4 - - + -
60A ARG* 3.5 28.7 - - - +
62A TYR* 4.6 2.5 - - - +
102A PHE* 4.3 9.6 - - + -
244A VAL* 3.1 35.4 + - + +
245A HIS* 4.2 8.7 - - - +
247A HIS* 1.3 77.6 - - + +
249A LEU* 1.3 60.0 + - + +
251A ALA* 2.9 4.6 + - - +
252A GLU* 2.9 53.0 + - + +
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Residues in contact with LEU 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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60A ARG* 4.7 3.4 - - - +
227A VAL* 3.6 17.0 - - + -
228A ILE 3.6 14.8 - - - +
229A GLY* 4.1 4.5 - - - -
245A HIS* 3.2 47.2 + - + +
246A GLY 3.8 2.2 - - - +
248A ILE* 1.3 72.5 - - + +
250A ALA* 1.3 66.0 + - - +
252A GLU* 3.4 24.7 + - + +
253A GLN* 3.0 30.8 + - + +
214B ILE* 3.5 26.5 - - + -
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Residues in contact with ALA 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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141A ILE* 4.9 3.1 - - + -
196A THR* 4.7 12.7 - - + +
198A ILE* 4.3 20.2 - - + -
227A VAL* 4.3 15.0 - - + +
246A GLY 3.0 14.0 + - - +
247A HIS* 3.2 15.3 - - - +
249A LEU* 1.3 74.8 - - - +
251A ALA* 1.3 57.4 + - - +
253A GLN* 3.1 4.2 + - - +
254A LEU* 2.9 29.0 + - - +
260A LEU* 4.4 6.2 - - + +
265A PHE* 6.3 1.1 - - + -
215B LEU* 4.9 4.3 - - + -
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Residues in contact with ALA 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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62A TYR* 5.8 2.5 - - + +
100A THR* 4.3 7.9 - - + -
102A PHE* 3.6 23.3 - - + -
139A LYS* 3.9 13.3 - - + +
141A ILE* 3.7 19.1 - - + -
247A HIS 2.9 12.0 + - - +
248A ILE* 2.9 9.3 + - - +
250A ALA* 1.3 71.4 - - - +
252A GLU* 1.3 60.4 + - + +
253A GLN 2.9 9.8 + - - -
254A LEU* 3.0 16.5 + - - +
255A SER 3.6 7.1 + - - -
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Residues in contact with GLU 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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38A LYS* 6.2 0.7 - - - +
60A ARG* 2.8 44.8 + - - -
62A TYR* 3.3 23.6 + - - +
139A LYS* 5.8 0.4 - - - +
248A ILE* 2.9 24.8 + - - +
249A LEU* 3.7 15.7 - - + +
251A ALA* 1.3 71.2 - - + +
253A GLN* 1.3 58.4 + - + +
255A SER* 3.2 18.9 + - - -
256A ARG* 3.6 29.8 + - - +
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Residues in contact with GLN 253 (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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227A VAL* 4.7 13.7 - - + -
249A LEU* 3.0 21.7 + - + +
250A ALA* 3.6 4.7 - - - +
251A ALA 2.9 1.2 - - - -
252A GLU* 1.3 78.4 - - + +
254A LEU* 1.3 60.3 + - - +
255A SER 3.0 2.2 - - - -
256A ARG* 2.8 54.9 + - - +
257A ASP* 2.9 40.9 + - - +
260A LEU* 3.8 17.4 - - + +
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Residues in contact with LEU 254 (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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139A LYS* 4.2 17.3 - - + -
140A LEU 5.0 1.6 - - - +
141A ILE* 5.2 4.3 - - + -
194A LEU* 3.3 68.6 - - + +
195A THR 4.1 4.9 - - - +
196A THR* 4.1 21.5 - - + +
250A ALA 2.9 13.4 + - - +
251A ALA* 3.0 10.7 + - - +
253A GLN* 1.3 76.2 - - - +
255A SER* 1.3 61.3 + - - +
257A ASP 3.5 16.6 - - - +
258A SER* 4.3 0.6 + - - -
260A LEU* 3.9 10.9 - - + +
261A GLY 3.7 25.4 - - - +
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Residues in contact with SER 255 (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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139A LYS* 4.4 20.9 - - - +
194A LEU* 5.4 1.1 - - - +
251A ALA 3.6 5.5 + - - -
252A GLU* 3.2 18.0 + - - -
253A GLN 3.0 0.6 - - - -
254A LEU* 1.3 79.6 - - - +
256A ARG* 1.3 79.2 + - - +
257A ASP* 4.6 0.5 - - - -
258A SER* 5.1 2.6 + - - -
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Residues in contact with ARG 256 (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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252A GLU* 3.6 28.4 + - - +
253A GLN* 2.8 39.0 + - - +
255A SER* 1.3 91.4 + - - +
257A ASP* 1.3 70.6 + - - +
258A SER 4.3 0.2 + - - -
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Residues in contact with ASP 257 (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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225A LYS* 5.7 2.4 - - - +
253A GLN* 2.9 26.3 + - - +
254A LEU* 3.5 15.7 - - - +
255A SER 4.8 0.2 - - - -
256A ARG* 1.3 88.6 - - - +
258A SER* 1.3 58.9 + - - +
259A THR* 2.9 25.6 + - - +
260A LEU* 3.4 13.9 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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