Contacts of the helix formed by residues 236 - 249 (chain A) in PDB entry 3H44
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 ASP 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A GLU* 4.0 12.1 - - - +
234A GLY 3.9 2.8 + - - -
235A ILE* 1.3 72.6 - - - +
237A VAL* 1.3 67.5 + - - +
238A ARG* 3.5 16.4 + - - +
239A GLN* 2.9 46.3 + - + +
240A GLU* 3.0 14.4 + - - +
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Residues in contact with VAL 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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103A ILE* 5.7 3.6 - - + -
106A LEU* 4.5 11.7 - - + -
109A PHE* 4.4 11.0 - - + -
179A LYS* 3.7 25.6 - - + +
226A LEU* 3.7 22.0 - - + +
227A GLU* 5.4 0.9 - - - -
230A PRO* 4.0 23.3 - - + -
231A ASN* 5.8 2.7 - - - +
235A ILE* 3.3 9.5 + - + +
236A ASP* 1.3 69.3 + - - +
238A ARG* 1.3 68.7 + - - +
239A GLN 2.9 1.1 - - - -
240A GLU* 2.7 9.2 + - + -
241A LEU* 2.7 40.7 + - + +
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Residues in contact with ARG 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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173A LEU* 2.9 32.4 + - - +
174A PHE* 3.1 24.4 + - + +
175A ASP* 4.8 0.4 - - - +
176A GLU* 3.2 35.6 - - - +
179A LYS* 4.0 8.8 - - + +
236A ASP* 3.4 7.4 + - - +
237A VAL* 1.3 77.7 - - - +
239A GLN* 1.3 64.7 + - - +
241A LEU* 4.0 10.5 - - - +
242A LEU* 3.1 59.1 + - - +
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Residues in contact with GLN 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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236A ASP* 2.9 41.5 + - + +
237A VAL 2.8 1.6 + - - -
238A ARG* 1.3 84.6 - - - +
240A GLU* 1.3 55.8 + - - +
242A LEU* 3.1 24.8 + - - +
243A LYS* 2.6 59.8 + - + +
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Residues in contact with GLU 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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100A PRO* 5.2 3.5 - - - +
102A ASN* 5.0 4.0 + - - +
103A ILE* 3.4 27.4 - - + +
106A LEU* 3.8 13.0 - - + +
235A ILE* 3.4 31.4 - - + -
236A ASP 3.0 5.0 + - - +
237A VAL* 2.7 15.6 + - + +
239A GLN* 1.3 73.6 - - - +
241A LEU* 1.3 58.5 + - - +
243A LYS* 3.7 14.5 - - - +
244A PHE* 2.8 34.5 + - - +
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Residues in contact with LEU 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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106A LEU* 3.8 21.3 - - + -
109A PHE* 4.3 10.3 - - + -
110A LEU* 3.5 47.9 - - + +
113A MET* 4.2 13.7 - - + -
174A PHE* 3.5 34.6 - - + -
179A LYS* 4.7 6.7 - - + -
237A VAL* 2.7 37.2 + - + +
238A ARG* 4.0 6.1 - - - +
240A GLU* 1.3 72.6 - - - +
242A LEU* 1.3 60.9 + - - +
244A PHE* 4.8 0.4 - - - -
245A HIS* 3.2 24.6 + - - +
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Residues in contact with LEU 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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172A PRO* 4.4 7.4 - - + +
174A PHE* 3.8 24.9 - - + -
238A ARG* 3.1 56.4 + - - +
239A GLN* 3.1 21.7 + - - +
241A LEU* 1.3 73.3 - - - +
243A LYS* 1.3 78.5 + - - +
245A HIS* 3.6 3.7 + - + +
246A SER* 3.1 27.0 + - - -
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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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239A GLN* 2.6 42.3 + - + +
240A GLU* 3.2 17.9 + - - +
242A LEU* 1.3 88.8 + - - +
244A PHE* 1.3 53.6 + - - +
246A SER* 3.3 11.9 + - - -
247A ALA* 2.8 36.3 + - - +
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Residues in contact with PHE 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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94A ILE* 3.7 20.0 - - + -
98A SER* 3.3 26.5 - - - -
99A ASP* 4.5 0.4 - - - -
100A PRO* 3.9 11.7 - - + -
106A LEU* 3.6 24.2 - - + -
107A SER* 3.6 31.2 - - - -
110A LEU* 3.7 18.2 - - + -
240A GLU 2.8 20.7 + - - +
241A LEU 4.4 1.8 - - - +
243A LYS* 1.3 74.0 - - - +
245A HIS* 1.3 55.7 + - - +
247A ALA* 4.3 5.4 - - - -
248A TYR* 3.0 51.2 + + + +
249A TYR* 4.2 15.3 - + - -
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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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110A LEU* 3.9 11.0 - - + -
114A LEU* 4.1 10.3 - - + -
168A PHE 3.1 22.1 + - - -
169A PHE* 4.0 16.0 - - - -
170A LEU 4.4 4.3 - - - -
172A PRO* 3.5 31.2 - - + +
174A PHE* 4.0 9.3 - + + -
241A LEU 3.2 19.8 + - - +
242A LEU* 3.8 5.2 - - - +
244A PHE* 1.3 77.2 - - - +
246A SER* 1.3 62.0 + - - +
249A TYR* 2.8 70.7 + + + +
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Residues in contact with SER 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 LEU 3.1 16.2 + - - -
243A LYS* 3.7 15.1 + - - -
245A HIS* 1.3 81.9 - - - +
247A ALA* 1.3 66.4 + - - +
249A TYR 4.9 3.3 + - - +
281A LYS* 3.0 40.5 + - - +
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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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243A LYS 2.8 17.2 + - - +
244A PHE* 3.7 6.5 - - - +
246A SER* 1.3 81.2 - - - +
248A TYR* 1.3 79.1 + - + +
250A SER* 4.2 3.1 - - - -
281A LYS* 4.3 5.6 - - - +
283A VAL* 3.2 23.4 - - - +
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Residues in contact with TYR 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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92A VAL* 4.1 9.5 - - - +
94A ILE* 3.4 44.4 - - + +
98A SER* 4.4 17.7 + - - -
100A PRO* 6.0 0.4 - - + -
244A PHE* 3.0 56.0 + + + +
247A ALA* 1.3 87.2 - - + +
249A TYR* 1.3 54.5 + - + +
250A SER* 2.5 24.5 + - - -
253A LEU* 4.2 5.7 - - - +
283A VAL* 4.1 22.4 - - + -
284A PRO 5.7 0.2 - - - -
286A PRO* 5.4 4.5 - - + -
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Residues in contact with TYR 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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92A VAL* 3.7 30.3 - - + -
94A ILE* 5.4 4.5 - - + -
107A SER* 4.9 4.2 + - - -
110A LEU* 3.5 19.2 - - + +
114A LEU* 4.0 6.3 - - + -
147A THR* 3.5 17.8 + - - +
149A TYR* 2.7 27.3 + - - -
169A PHE* 3.7 34.1 - + - +
244A PHE* 4.2 18.8 - + - -
245A HIS* 2.8 55.9 + + + +
246A SER* 5.1 2.8 - - - +
247A ALA 5.0 0.4 - - - -
248A TYR* 1.3 72.3 - - + +
250A SER* 1.3 56.7 + - - +
251A SER 4.3 0.2 + - - -
254A MET* 3.6 14.5 - - + +
278A VAL* 4.7 5.2 - - - +
279A GLU 4.6 2.6 - - - +
281A LYS* 5.7 1.6 + - - -
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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