Contacts of the helix formed by residues 246 - 260 (chain A) in PDB entry 4WTJ
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 PRO 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ALA 3.5 15.9 - - - +
81A ARG* 4.5 4.7 - - + -
82A LEU* 3.9 35.7 - - + +
245A LEU* 1.3 87.5 - - + +
247A GLU* 1.3 67.2 + - - +
248A GLU* 4.4 4.0 - - + +
249A ALA* 3.1 18.5 + - + +
250A ARG* 3.3 9.4 + - - +
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LEU 3.7 0.8 + - - -
246A PRO* 1.3 74.1 - - - +
248A GLU* 1.3 62.1 + - - +
250A ARG* 3.2 30.4 + - - +
251A THR* 3.0 31.5 + - - +
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Residues in contact with GLU 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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82A LEU* 3.6 25.1 - - + +
123A TRP* 2.9 30.2 + - + -
127A LEU* 3.7 26.2 - - + +
246A PRO* 3.2 2.8 - - + +
247A GLU* 1.3 81.4 - - - +
249A ALA* 1.3 61.6 + - - +
251A THR* 3.3 8.9 + - - -
252A ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 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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81A ARG 5.7 0.7 - - - -
82A LEU* 3.7 28.1 - - + +
123A TRP* 5.3 0.2 - - - -
174A ALA* 4.5 6.3 - - - +
245A LEU* 4.2 11.2 - - + -
246A PRO* 3.1 24.0 + - + +
248A GLU* 1.3 75.4 - - - +
250A ARG* 1.3 57.8 + - - +
252A ALA* 3.0 5.9 + - - +
253A ILE* 2.7 50.6 + - + +
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Residues in contact with ARG 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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241A GLN* 2.7 76.8 + - - +
243A CYS 2.9 21.8 + - - -
244A SER* 3.8 3.6 - - - +
245A LEU* 3.4 31.9 + - + +
246A PRO 3.6 11.0 - - - +
247A GLU* 3.2 33.3 + - - +
249A ALA* 1.3 75.1 - - - +
251A THR* 1.3 58.0 + - - +
253A ILE* 4.5 2.7 - - - +
254A HIS* 2.9 28.8 + - - +
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Residues in contact with THR 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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126A LEU 4.7 1.3 - - - +
127A LEU* 3.8 37.5 - - + +
247A GLU* 3.0 20.1 + - - +
248A GLU* 3.5 9.4 - - - -
249A ALA 3.1 0.2 - - - -
250A ARG* 1.3 79.9 - - - +
252A ALA* 1.3 61.3 + - - +
254A HIS* 3.4 5.6 + - - +
255A SER* 3.0 23.7 + - - -
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Residues in contact with ALA 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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123A TRP* 3.4 39.7 - - + -
126A LEU* 4.9 10.8 - - + -
127A LEU* 4.1 8.5 - - + +
174A ALA* 4.0 7.4 - - + -
248A GLU 3.1 9.2 + - - +
249A ALA 3.0 6.5 + - - +
251A THR* 1.3 76.6 - - - +
253A ILE* 1.3 53.7 + - - +
255A SER* 3.2 6.1 + - - -
256A LEU* 2.8 40.7 + - - +
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Residues in contact with ILE 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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174A ALA* 3.8 22.0 - - + +
175A LEU* 3.8 27.8 - - + -
178A ILE* 4.0 4.0 - - + -
237A GLU* 3.8 21.5 - - + -
240A TYR* 4.2 22.0 - - + -
241A GLN* 3.9 7.6 - - - +
245A LEU* 3.6 30.3 - - + -
249A ALA* 2.7 27.8 + - + +
250A ARG* 3.6 3.1 - - - +
252A ALA* 1.3 73.3 - - - +
254A HIS* 1.3 56.9 + - - +
256A LEU* 3.7 7.4 - - - +
257A THR* 2.9 34.9 + - - +
261A TYR* 5.3 0.7 - - - -
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Residues in contact with HIS 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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130A PRO* 5.6 8.5 - - + -
237A GLU* 2.2 40.9 + - - +
241A GLN* 4.3 2.9 + - - +
250A ARG 2.9 17.6 + - - +
251A THR* 3.9 5.6 - - - +
253A ILE* 1.3 76.0 - - - +
255A SER* 1.3 56.8 + - - +
257A THR* 3.3 2.8 + - - -
258A GLU* 2.9 54.6 + - + +
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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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126A LEU* 3.0 36.3 + - - +
129A ASP 3.0 17.6 + - - -
130A PRO* 4.2 16.4 - - - +
251A THR* 3.0 15.6 + - - -
252A ALA* 3.6 4.0 - - - -
254A HIS* 1.3 76.8 - - - +
256A LEU* 1.3 61.0 + - - +
259A ARG* 2.8 43.1 + - - +
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Residues in contact with LEU 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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126A LEU* 3.9 33.4 - - + -
134A ILE* 4.7 2.9 - - + -
167A VAL* 4.4 6.7 - - + -
170A CYS 4.6 0.2 - - - +
171A GLU* 4.0 32.5 - - + +
174A ALA* 3.9 25.6 - - + -
175A LEU* 4.2 4.7 - - + -
252A ALA 2.8 23.2 + - - +
253A ILE* 3.7 3.8 - - - +
255A SER* 1.3 68.9 - - - +
257A THR* 1.3 62.1 + - - +
259A ARG* 5.0 1.1 - - - -
260A LEU* 2.8 43.2 + - + +
261A TYR* 3.0 30.9 + - + +
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Residues in contact with THR 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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233A ILE* 4.3 12.1 + - + +
234A ARG* 4.4 4.3 - - - -
237A GLU* 3.3 45.0 - - + +
240A TYR* 5.2 2.4 - - - -
253A ILE* 2.9 25.7 + - - +
254A HIS 3.4 1.3 - - - -
256A LEU* 1.3 78.9 - - - +
258A GLU* 1.3 67.4 + - - +
261A TYR* 3.3 17.5 + - - -
262A VAL* 3.0 44.7 + - + +
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Residues in contact with GLU 258 (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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130A PRO 3.5 21.1 - - - +
131A GLN* 4.6 6.5 - - - +
133A PRO* 5.4 1.9 - - - +
234A ARG* 2.9 51.9 + - - +
237A GLU* 4.4 1.6 - - - +
254A HIS* 2.9 46.9 + - + +
257A THR* 1.3 79.9 - - + +
259A ARG* 1.3 60.8 + - - +
262A VAL* 3.5 14.2 - - - +
263A GLY 4.9 0.9 - - - +
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Residues in contact with ARG 259 (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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125A ASP* 2.9 42.6 + - - -
126A LEU* 3.7 7.9 - - - +
129A ASP* 2.7 50.0 + - - +
130A PRO 3.7 2.5 - - - -
131A GLN 3.5 22.0 - - - +
132A THR* 2.5 33.8 + - - +
133A PRO* 3.5 7.2 + - - +
134A ILE* 2.9 53.9 + - + +
255A SER* 2.8 25.7 + - - +
258A GLU* 1.3 80.7 - - - +
260A LEU* 1.3 58.2 + - - +
263A GLY 3.5 10.0 - - - +
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Residues in contact with LEU 260 (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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134A ILE* 4.4 16.6 - - + +
136A THR* 3.7 30.1 - - + -
163A PRO* 3.8 28.9 - - + -
167A VAL* 3.9 17.7 - - + -
171A GLU* 4.0 7.2 - - - -
256A LEU* 2.8 22.3 + - + +
258A GLU 3.6 0.4 - - - -
259A ARG* 1.3 75.3 - - - +
261A TYR* 1.3 87.1 + - + +
262A VAL 3.4 1.3 - - - -
263A GLY 3.1 5.2 - - - +
277A ARG* 2.6 31.8 + - - +
281A ALA* 5.2 0.4 - - + +
284A VAL* 3.9 11.0 - - + -
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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