Contacts of the helix formed by residues 238 - 252 (chain A) in PDB entry 6QHD
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 GLU 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.0 39.8 + - - +
233A LYS* 4.1 4.9 - - - +
234A THR* 3.2 32.7 + - - +
236A THR 3.3 1.0 - - - -
237A ASP* 1.3 89.9 - - + +
239A GLU* 1.3 67.5 + - - +
240A LEU 3.5 0.4 - - - -
241A ALA* 4.0 1.6 - - - +
242A ASP* 3.1 34.4 + - - +
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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
----------------------------------------------------------
138A THR* 4.6 2.8 + - - -
140A LYS* 4.0 27.4 + - + +
141A GLN* 3.2 39.6 + - + +
144A LEU* 4.1 24.5 - - + -
234A THR* 3.0 17.4 + - + +
235A LEU 3.8 7.0 - - - +
238A GLU* 1.3 76.6 - - - +
240A LEU* 1.3 63.1 + - - +
242A ASP* 3.4 15.0 + - - +
243A TRP* 3.2 20.4 + - - +
246A ARG* 4.9 5.2 + - - -
263A LEU* 4.0 15.5 - - + +
266A TRP* 4.6 5.5 - - + -
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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
----------------------------------------------------------
235A LEU 3.0 12.4 + - - +
236A THR* 3.3 20.2 - - + +
239A GLU* 1.3 72.6 - - - +
241A ALA* 1.3 66.5 + - - +
243A TRP* 3.1 17.8 + - + +
244A LYS* 3.0 36.0 + - + +
263A LEU* 3.8 27.1 - - + +
267A ILE* 4.8 10.1 - - + -
319A SER* 3.4 38.4 - - - +
322A VAL* 4.6 5.2 - - + -
352A LEU* 4.2 19.3 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR 3.8 5.3 + - - +
237A ASP* 3.7 26.7 - - - +
238A GLU 3.7 1.8 + - - +
239A GLU 3.3 0.2 - - - -
240A LEU* 1.3 79.4 - - - +
242A ASP* 1.3 63.6 + - - +
244A LYS* 3.5 15.5 + - + +
245A ARG* 3.3 18.0 + - - +
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Residues in contact with ASP 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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140A LYS* 5.3 2.8 + - - -
238A GLU* 3.1 27.6 + - - +
239A GLU* 3.8 16.4 - - - +
240A LEU 3.1 0.4 - - - -
241A ALA* 1.3 77.7 - - - +
243A TRP* 1.3 64.8 + - - +
244A LYS 3.1 0.2 - - - -
245A ARG* 3.1 7.7 + - - +
246A ARG* 3.0 43.1 + - + +
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Residues in contact with TRP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU 3.2 6.1 + - - +
240A LEU* 3.1 13.9 + - + +
242A ASP* 1.3 76.6 - - - +
244A LYS* 1.3 88.0 + - + +
246A ARG* 3.0 30.4 + - - +
247A GLN* 2.9 59.0 + - + +
257A ASN 4.2 1.3 - - - -
258A ILE* 2.6 44.9 + - + +
259A CYS 4.0 7.9 - - - -
260A LEU* 3.4 42.7 - - + +
263A LEU* 3.6 20.6 - - + -
322A VAL* 4.5 17.3 - - + -
323A VAL 3.7 11.0 - - - -
324A GLU* 4.8 4.0 - - + -
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Residues in contact with LYS 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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240A LEU* 3.0 34.5 + - + +
241A ALA* 3.6 17.0 - - - +
242A ASP 3.1 0.2 - - - -
243A TRP* 1.3 90.6 - - + +
245A ARG* 1.3 64.2 + - - +
247A GLN* 3.3 23.4 - - - +
248A GLN* 3.3 14.1 + - - +
319A SER* 4.6 2.8 + - - +
321A PHE 5.2 1.6 + - - -
322A VAL* 3.6 28.5 - - - +
456A THR* 5.9 0.8 + - - -
459A LEU* 5.8 0.3 - - - +
487A PRO* 6.6 0.4 - - - -
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Residues in contact with ARG 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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241A ALA 3.3 9.2 + - - +
242A ASP* 3.1 12.1 + - - +
244A LYS* 1.3 76.1 - - - +
246A ARG* 1.3 68.9 + - + +
248A GLN* 3.0 45.1 + - - +
249A ILE* 3.2 43.6 + - + +
481A ASN 2.3 31.9 + - - -
482A MET* 4.1 11.5 + - - +
484A THR 3.1 21.2 + - - +
485A ASN* 4.0 16.1 - - + +
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Residues in contact with ARG 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 5.6 6.6 - - - +
239A GLU* 4.9 6.1 + - - -
242A ASP* 3.0 40.5 + - + +
243A TRP* 3.0 32.1 + - - +
245A ARG* 1.3 79.4 - - + +
247A GLN* 1.3 55.8 + - - +
249A ILE* 3.3 11.9 + - + +
250A ALA* 2.9 22.0 + - - +
255A PRO 4.6 6.9 - - - +
257A ASN* 2.9 50.2 + - - +
258A ILE* 3.3 10.8 - - + +
259A CYS 5.0 4.6 + - - -
263A LEU* 5.5 2.0 - - - +
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Residues in contact with GLN 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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243A TRP* 2.9 33.2 + - + +
244A LYS* 3.3 16.4 - - - +
245A ARG 3.1 0.2 - - - -
246A ARG* 1.3 74.4 - - - +
248A GLN* 1.3 65.4 + - + +
250A ALA* 3.1 3.3 + - + +
251A CYS* 3.0 31.5 + - - -
258A ILE* 3.7 16.9 - - + +
323A VAL 2.9 26.4 + - - +
324A GLU 3.2 18.6 + - - -
326A GLN* 3.1 38.6 + - + +
459A LEU* 5.2 2.8 - - + +
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Residues in contact with GLN 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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244A LYS 3.5 11.9 - - - +
245A ARG* 3.0 41.6 + - - +
247A GLN* 1.3 80.1 - - - +
249A ILE* 1.3 59.6 + - - +
251A CYS* 3.6 7.0 + - - +
252A ILE* 3.5 22.0 + - - +
459A LEU* 4.1 27.3 - - + +
480A TYR* 4.5 6.1 - - - -
481A ASN* 2.8 38.9 + - + +
484A THR 3.0 21.4 + - - -
485A ASN* 3.6 20.2 - - - +
486A ASN 4.8 0.8 + - - -
487A PRO* 6.3 0.2 - - - -
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Residues in contact with ILE 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 ARG* 3.2 51.4 + - + +
246A ARG* 3.8 10.5 - - + +
247A GLN 3.2 0.6 - - - -
248A GLN* 1.3 76.3 - - - +
250A ALA* 1.3 59.2 + - - +
252A ILE* 3.6 11.3 - - + +
253A GLY 3.3 3.8 + - - -
254A GLY* 2.5 51.8 + - - -
255A PRO* 4.3 11.2 - - + +
481A ASN 5.4 0.4 - - - +
482A MET* 6.5 0.2 - - - -
510A TRP* 3.7 21.1 - - + -
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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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246A ARG 2.9 14.7 + - - +
247A GLN* 3.1 8.9 + - + +
249A ILE* 1.3 80.8 - - - +
251A CYS* 1.3 58.5 - - - +
253A GLY* 3.0 19.1 + - - -
254A GLY 3.9 11.0 + - - +
255A PRO 4.7 0.9 - - - -
256A PRO* 4.3 13.5 - - + +
258A ILE* 3.5 23.6 - - + -
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Residues in contact with CYS 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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247A GLN* 3.0 31.1 + - - +
248A GLN* 3.8 6.5 - - - +
249A ILE 3.3 0.4 - - - -
250A ALA* 1.3 77.7 - - - +
252A ILE* 1.3 66.1 + - + +
253A GLY 3.2 1.0 + - - -
326A GLN* 4.2 27.4 - - - -
334A ASP 4.3 2.8 - - - +
336A PRO* 3.7 31.4 - - + +
337A LEU* 4.6 8.7 - - + -
459A LEU* 4.5 8.5 - - + -
474A TRP* 3.4 16.1 - - + -
477A ILE* 5.8 0.4 - - + -
481A ASN* 5.5 0.7 - - - +
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Residues in contact with ILE 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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248A GLN 3.5 20.2 - - - +
249A ILE* 3.6 13.7 - - + +
251A CYS* 1.3 80.2 - - + +
253A GLY* 1.3 56.4 + - - +
474A TRP* 4.0 9.0 - - + -
477A ILE* 3.9 21.5 - - + +
478A LEU* 3.8 19.7 - - + +
481A ASN* 3.8 16.4 - - + -
482A MET* 3.9 23.8 - - - +
507A VAL* 4.2 15.7 - - + -
510A TRP* 3.9 23.6 - - + -
511A GLN* 3.0 25.4 + - - -
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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