Contacts of the helix formed by residues 233 - 245 (chain A) in PDB entry 4XQ2
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A VAL 4.0 0.2 + - - -
232A PRO* 1.3 77.0 - - - +
234A ALA* 1.3 61.7 + - - -
235A LEU 3.3 2.5 - - - -
236A ASP* 3.2 24.0 + - - +
237A CYS* 2.9 31.0 + - - -
206B LEU* 6.3 3.6 - - - -
236B ASP* 3.4 16.6 - - - -
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Residues in contact with ALA 234 (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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28A ILE* 4.1 5.1 - - + +
29A HIS 3.1 28.3 - - - +
30A VAL* 3.8 20.2 - - + -
51A ASN* 4.2 13.0 - - - +
53A THR* 3.6 14.9 - - - +
54A ARG* 6.3 0.2 - - - -
232A PRO 4.0 0.4 + - - -
233A GLY* 1.3 70.5 - - - -
235A LEU* 1.3 58.8 + - + +
237A CYS* 3.4 5.5 + - - -
238A PHE* 3.1 23.4 + - - +
236B ASP* 4.5 2.4 + - - -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.0 27.8 - - + -
30A VAL* 4.1 16.8 - - + -
233A GLY 3.3 0.4 - - - -
234A ALA* 1.3 72.8 - - - +
236A ASP* 1.3 66.7 + - - +
238A PHE* 3.2 9.3 + - + +
239A LEU* 3.1 26.8 + - - +
235B LEU* 4.3 27.4 - - + -
236B ASP* 3.8 14.7 + - - +
239B LEU* 3.6 31.6 - - + -
28C ILE* 4.6 9.9 - - + -
235C LEU* 4.7 10.3 - - + -
238C PHE* 6.1 2.0 - - + -
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Residues in contact with ASP 236 (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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205A VAL* 3.6 25.4 - - + +
206A LEU* 4.5 8.5 + - - +
232A PRO* 4.6 7.4 - - + -
233A GLY* 3.2 33.1 + - - +
235A LEU* 1.3 76.9 - - - +
237A CYS* 1.3 61.9 + - - +
239A LEU* 3.2 8.1 + - - +
240A VAL* 3.1 26.5 + - - +
233B GLY* 3.2 28.6 - - - -
235B LEU* 5.3 5.3 + - - +
236B ASP* 3.8 17.2 + - - +
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Residues in contact with CYS 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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53A THR* 3.9 16.8 - - + +
54A ARG* 3.7 28.0 - - - +
57A LEU* 4.0 24.9 - - + +
232A PRO* 3.6 28.0 - - - -
233A GLY 2.9 21.4 + - - +
234A ALA* 3.6 6.7 - - - +
235A LEU 3.3 0.2 - - - -
236A ASP* 1.3 73.9 - - - +
238A PHE* 1.3 64.7 + - - +
240A VAL* 3.4 3.5 + - - +
241A ARG* 2.9 25.9 + - - +
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Residues in contact with PHE 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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25A VAL* 4.3 13.9 - - + -
26A PRO 5.1 4.3 - - - -
28A ILE* 3.7 34.5 - - + -
53A THR* 4.2 8.8 - - + +
234A ALA 3.1 13.7 + - - +
235A LEU* 3.2 10.7 + - + +
237A CYS* 1.3 76.0 - - - +
239A LEU* 1.3 74.9 + - + +
241A ARG* 3.6 7.8 - - + +
242A ARG* 2.9 58.8 + - + +
30C VAL* 4.1 28.9 - - + -
235C LEU* 6.3 2.5 - - + -
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Residues in contact with LEU 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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200A ALA* 4.7 3.3 - - - +
204A ASP* 4.3 36.7 - - + +
205A VAL* 4.1 18.6 - - + -
235A LEU 3.1 14.3 + - - +
236A ASP* 3.2 7.6 + - - +
238A PHE* 1.3 91.3 - - + +
240A VAL* 1.3 59.0 + - - +
242A ARG* 3.5 10.5 + - - +
243A GLY* 3.0 24.3 + - - -
30B VAL* 5.6 2.5 - - + -
235B LEU* 3.7 28.7 - - + -
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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
----------------------------------------------------------
57A LEU* 3.9 26.0 - - + -
195A THR* 3.9 33.4 - - + +
199A ILE* 4.0 14.4 - - + +
200A ALA* 4.1 12.1 - - + -
205A VAL* 3.8 20.6 - - + -
207A GLY* 5.1 7.2 - - - +
236A ASP* 3.1 16.5 + - + +
237A CYS* 3.4 7.2 + - - +
239A LEU* 1.3 71.6 - - - +
241A ARG* 1.3 61.0 + - - +
243A GLY* 3.1 2.4 + - - -
244A LEU* 2.9 28.5 + - + +
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Residues in contact with ARG 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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10A LEU 3.0 23.0 + - - -
11A VAL 3.0 28.5 + - - -
12A HIS 4.1 0.4 - - - -
13A GLY 2.9 30.0 + - - +
14A GLY 5.2 2.2 + - - -
15A ARG* 4.8 6.4 - - - +
26A PRO* 6.3 3.5 - - + +
53A THR* 6.1 0.7 - - + +
56A GLU* 4.6 6.5 + - + +
57A LEU* 4.0 25.3 - - + +
60A CYS* 3.7 22.2 - - - +
237A CYS 2.9 17.9 + - - +
238A PHE* 3.6 9.2 - - + +
240A VAL* 1.3 75.7 - - - +
242A ARG* 1.3 65.0 + - - +
244A LEU* 3.2 15.1 - - - +
245A HIS* 3.6 16.2 + - - +
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Residues in contact with ARG 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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202A HIS* 5.5 1.6 - - - -
238A PHE* 2.9 46.2 + - + +
239A LEU* 3.8 13.0 - - - +
241A ARG* 1.3 77.8 - - - +
243A GLY* 1.3 63.7 + - - +
245A HIS* 3.5 27.3 + - + +
246A THR* 5.0 1.7 + - - +
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Residues in contact with GLY 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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199A ILE 3.7 0.2 - - - -
200A ALA 3.3 22.9 - - - -
202A HIS* 4.0 11.4 - - - -
239A LEU 3.0 13.1 + - - -
240A VAL 3.1 3.3 + - - -
242A ARG* 1.3 77.1 - - - +
244A LEU* 1.3 62.2 + - - +
245A HIS 2.9 2.1 + - - -
246A THR* 3.1 13.9 + - - -
250A ARG* 3.1 20.8 + - - -
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Residues in contact with LEU 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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10A LEU* 3.3 36.3 - - + +
57A LEU* 3.6 24.9 - - + -
60A CYS* 4.3 14.4 - - - -
61A LEU* 3.6 23.8 - - + -
64A LEU* 3.9 8.7 - - + -
199A ILE* 3.3 31.4 + - + +
240A VAL* 2.9 15.1 + - + +
241A ARG* 3.2 18.4 - - - +
243A GLY* 1.3 70.1 - - - +
245A HIS* 1.3 63.9 + - - +
247A LEU* 3.0 34.7 + - + +
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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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7A GLY 5.2 0.3 - - - +
10A LEU* 3.5 22.2 + - - +
11A VAL* 3.2 58.6 - - + +
15A ARG* 5.1 6.3 - - - -
25A VAL* 6.0 5.0 - - + +
241A ARG* 3.6 27.4 + - - +
242A ARG* 3.5 32.3 + - + +
243A GLY 2.9 4.6 + - - -
244A LEU* 1.3 74.8 - - - +
246A THR* 1.3 66.1 + - + +
249A LEU* 5.6 2.9 - - - +
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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
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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