Contacts of the helix formed by residues 245 - 260 (chain A) in PDB entry 2DOU
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 SER 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 5.9 0.2 - - - -
193A TRP* 3.4 15.5 - - - -
219A LYS 3.2 24.0 + - - -
220A GLU 3.9 6.9 + - - -
222A VAL 2.9 21.2 + - - -
223A VAL* 4.4 0.8 - - - +
244A GLY* 1.3 71.6 - - - +
246A GLU* 1.3 64.1 + - - +
247A GLU* 3.3 6.6 + - - +
248A ALA* 2.8 32.0 + - - +
249A LEU* 2.9 22.9 + - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 2.8 78.1 + - + +
89A GLU* 4.4 8.7 + - + +
219A LYS 4.2 2.8 + - - -
244A GLY 3.1 3.2 + - - -
245A SER* 1.3 72.5 - - - +
247A GLU* 1.3 63.5 + - - +
249A LEU* 3.9 1.3 - - - +
250A ALA* 3.1 25.0 + - + +
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Residues in contact with GLU 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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193A TRP* 3.7 25.1 - - + -
220A GLU 4.9 4.7 - - - +
245A SER* 3.2 7.1 + - - +
246A GLU* 1.3 83.4 - - - +
248A ALA* 1.3 64.2 + - - +
250A ALA* 3.4 11.0 + - - +
251A ARG* 3.4 27.5 + - - +
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Residues in contact with ALA 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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103A LEU* 4.8 1.1 - - + -
107A LEU* 3.9 23.8 - - + +
193A TRP* 3.7 15.8 - - + -
223A VAL* 3.4 28.9 - - + -
245A SER* 2.8 20.1 + - - +
247A GLU* 1.3 77.1 - - - +
249A LEU* 1.3 59.1 + - - +
251A ARG* 2.9 21.3 + - - +
252A LEU* 3.0 11.9 + - - +
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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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88A ARG 4.4 6.3 - - - +
89A GLU* 3.3 37.0 - - - +
90A ALA* 3.3 17.9 - - - +
91A LEU* 4.0 8.5 - - + +
103A LEU* 5.4 0.4 - - + -
223A VAL* 3.8 20.4 - - + -
242A ALA* 3.8 28.7 - - + +
244A GLY 3.9 11.4 - - - +
245A SER 2.9 18.2 + - - +
246A GLU 4.1 2.9 - - - +
248A ALA* 1.3 76.9 - - - +
250A ALA* 1.3 56.9 + - - +
252A LEU* 3.6 15.5 - - + +
253A GLU* 2.7 31.7 + - - +
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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 GLU* 3.1 20.9 + - + +
247A GLU* 3.7 7.0 - - - +
248A ALA 3.2 0.2 - - - -
249A LEU* 1.3 76.0 - - - +
251A ARG* 1.3 62.9 + - + +
253A GLU* 3.8 12.2 - - - +
254A ARG* 3.1 22.0 + - - +
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Residues in contact with ARG 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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106A ALA* 3.5 29.9 + - + +
107A LEU* 3.7 25.1 + - + +
193A TRP* 3.6 33.3 - - - +
247A GLU* 3.4 26.4 + - + +
248A ALA* 2.9 7.9 + - - +
250A ALA* 1.3 78.0 - - + +
252A LEU* 1.3 66.3 + - - +
254A ARG* 3.1 16.3 + - - +
255A VAL* 3.1 11.3 + - - +
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Residues in contact with LEU 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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91A LEU* 3.7 19.3 - - + -
93A LEU* 4.2 18.8 - - + -
99A GLY* 4.1 8.5 - - - +
102A HIS* 3.8 13.5 - - + -
103A LEU* 3.7 43.7 - - + +
106A ALA* 3.6 7.8 - - - +
225A LEU* 5.5 0.4 - - + -
242A ALA* 4.3 4.9 - - + -
248A ALA 3.0 11.3 + - - +
249A LEU* 3.6 24.9 - - + +
251A ARG* 1.3 77.3 - - - +
253A GLU* 1.3 60.6 + - - +
255A VAL* 3.1 2.3 + - + +
256A LYS* 2.9 36.5 + - + +
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Residues in contact with GLU 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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62A LYS* 3.3 43.6 + - - +
91A LEU* 3.6 25.6 - - + +
249A LEU 2.7 22.2 + - - +
250A ALA* 3.8 11.3 - - - +
252A LEU* 1.3 72.7 - - - +
254A ARG* 1.3 57.9 + - - +
256A LYS* 3.9 3.7 - - - +
257A GLY* 3.0 26.2 + - - -
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Residues in contact with ARG 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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250A ALA 3.1 14.0 + - - +
251A ARG* 3.1 12.2 + - - +
253A GLU* 1.3 77.0 - - - +
255A VAL* 1.3 76.1 + - + +
257A GLY* 3.4 7.7 + - - -
258A VAL* 3.5 21.0 + - - +
126B GLY* 4.1 22.0 + - - -
129B ARG* 4.3 15.6 - - - +
130B VAL* 4.5 8.9 - - - +
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Residues in contact with VAL 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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102A HIS* 3.9 25.4 - - + +
105A LEU* 4.7 4.9 - - + -
106A ALA* 3.6 35.2 - - + +
251A ARG 3.1 3.5 + - - +
252A LEU 3.1 7.5 + - - +
254A ARG* 1.3 83.5 - - + +
256A LYS* 1.3 68.1 + - - +
257A GLY 3.0 1.3 - - - -
258A VAL* 3.0 26.8 + - - +
259A ILE* 3.3 27.1 + - + +
130B VAL* 4.6 15.9 - - + -
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Residues in contact with LYS 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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91A LEU* 4.2 11.4 - - + -
92A ALA 3.5 23.1 + - - -
93A LEU* 4.4 4.9 - - + -
94A ILE* 4.0 8.7 - - - +
98A GLU* 2.7 45.8 + - - +
102A HIS* 4.3 5.2 - - + +
252A LEU* 2.9 41.9 + - + +
253A GLU* 4.2 4.5 - - - +
255A VAL* 1.3 76.6 - - - +
257A GLY* 1.3 56.3 + - - +
259A ILE* 4.3 5.2 - - - -
260A ASP* 2.7 67.8 + - - +
262A ASN* 4.5 8.0 + - - -
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Residues in contact with GLY 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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253A GLU 3.0 19.0 + - - -
254A ARG* 3.8 3.6 - - - -
255A VAL 3.0 0.8 - - - -
256A LYS* 1.3 78.3 - - - +
258A VAL* 1.3 61.0 + - - +
259A ILE 3.8 0.3 + - - -
260A ASP 4.0 9.7 - - - +
261A PHE* 5.4 2.6 - - - -
97B GLN* 4.0 7.1 + - - +
123B SER* 4.8 1.6 - - - -
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Residues in contact with VAL 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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254A ARG* 3.5 26.0 + - - +
255A VAL* 3.0 15.5 - - - +
257A GLY* 1.3 77.1 - - - +
259A ILE* 1.3 63.6 + - + +
97B GLN* 3.5 16.8 - - - +
100B LEU* 5.8 0.7 - - - +
101B ALA* 4.4 6.1 - - - +
123B SER* 3.7 25.7 - - - +
126B GLY* 3.9 20.0 - - - -
127B ALA* 4.1 11.2 - - - +
130B VAL* 3.5 29.8 - - + -
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Residues in contact with ILE 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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102A HIS* 3.6 35.9 - - + +
105A LEU* 5.2 0.9 - - + -
255A VAL* 3.4 27.6 - - + +
256A LYS* 3.1 5.1 + - - +
258A VAL* 1.3 86.0 - - + +
260A ASP* 1.3 64.8 + - + +
97B GLN* 3.3 7.3 - - - +
98B GLU* 3.1 33.5 + - + +
101B ALA* 3.5 24.0 - - + -
102B HIS* 3.9 28.9 - - + +
105B LEU* 5.5 0.7 - - + -
130B VAL* 4.4 13.9 - - + -
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Residues in contact with ASP 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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94A ILE* 3.6 23.2 - - + +
98A GLU* 4.1 4.0 - - - +
102A HIS* 5.0 0.3 + - - -
256A LYS* 2.7 62.4 + - - +
257A GLY* 4.0 7.1 - - - +
259A ILE* 1.3 81.8 - - + +
261A PHE* 1.3 75.0 + - - +
262A ASN* 2.6 30.3 + - - +
94B ILE 5.6 2.0 - - - +
97B GLN* 3.4 10.9 - - - +
98B GLU* 5.2 6.7 - - + -
238B ARG* 4.8 5.4 - - - +
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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