Contacts of the helix formed by residues 115 - 123 (chain D) in PDB entry 2EHO
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 HIS 115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016B SO4 4.7 8.7 - - - -
23D ASP* 4.1 15.5 + - + -
26D LEU* 4.2 12.4 - - + +
27D MSE 3.5 55.6 + - + +
30D GLU* 4.6 9.5 + - + -
113D GLY* 3.1 2.8 - - - -
114D PRO* 1.3 89.0 - - + +
116D PHE* 1.3 65.3 + - - +
117D TYR 3.2 2.8 + - - -
118D GLY* 3.3 3.9 + - - +
119D PHE* 2.9 25.7 + - + +
169D ASP* 3.5 5.8 - - - -
170D GLU* 3.8 33.3 + - + +
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ILE* 3.6 25.8 - - + -
92D TYR* 2.9 46.9 + + - -
100D PHE* 3.3 35.4 - + - -
109D LEU* 3.6 35.2 - - + -
112D MSE 5.1 2.2 - - + -
113D GLY 3.0 16.6 + - - +
114D PRO 3.3 0.2 - - - -
115D HIS* 1.3 73.7 - - - +
117D TYR* 1.3 74.0 + + - +
120D GLY* 3.2 7.6 + - - -
137D SER 5.9 0.4 - - - -
138D LEU* 3.7 25.5 - - + +
141D THR* 4.0 15.7 - - + -
169D ASP* 3.1 12.2 + - + +
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Residues in contact with TYR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 3.7 13.1 - - + +
13D LEU* 4.2 11.7 - - + +
109D LEU* 3.5 20.7 - - + +
115D HIS 3.3 0.8 - - - -
116D PHE* 1.3 81.6 - + - +
118D GLY* 1.3 66.0 + - - +
120D GLY* 3.3 2.1 + - - -
121D SER* 3.0 24.3 + - - -
138D LEU* 3.3 36.6 - - + +
141D THR* 3.1 29.3 + - - -
142D PHE* 3.3 20.3 - + + -
169D ASP* 3.3 23.5 + - - -
171D MSE 3.4 23.3 - - + -
172D GLU* 2.8 33.2 + - + -
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Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA* 3.6 14.5 - - - +
13D LEU* 3.6 21.3 - - - +
27D MSE 4.2 11.0 - - - -
115D HIS* 3.3 6.6 + - - +
117D TYR* 1.3 78.8 - - - +
119D PHE* 1.3 61.9 + - - +
121D SER* 3.3 4.2 + - - -
122D GLN* 3.2 23.4 + - - +
169D ASP* 4.9 1.0 + - - -
171D MSE 5.7 1.2 - - - +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D MSE 3.9 25.2 - - + +
30D GLU* 3.5 35.4 - - + -
31D LYS 3.7 10.3 - - - -
32D LEU* 3.8 20.2 - - + -
70D LEU* 3.3 43.1 - - + +
89D PRO* 4.5 8.1 - - + -
92D TYR* 3.5 23.8 - + - +
113D GLY* 6.3 1.1 - - - -
115D HIS* 2.9 19.9 + - + +
118D GLY* 1.3 71.3 - - - +
120D GLY* 1.3 67.8 + - - +
122D GLN* 3.2 2.1 + - - +
123D LEU* 2.8 34.6 + - + +
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Residues in contact with GLY 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D TYR* 3.5 27.7 + - - -
116D PHE 3.2 9.4 + - - -
117D TYR 3.7 3.8 - - - -
118D GLY 3.3 0.2 - - - -
119D PHE* 1.3 79.8 - - - +
121D SER* 1.3 57.9 + - - +
123D LEU* 3.2 11.8 - - - +
124D LEU* 2.8 23.6 - - - +
134D ILE* 4.6 3.1 - - - +
138D LEU* 3.9 12.5 - - - +
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Residues in contact with SER 121 (chain D).
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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170C LEU* 4.7 4.5 - - - -
173C ASN* 4.4 7.5 - - - +
12D ALA 3.0 22.5 + - - -
13D LEU* 3.4 14.3 + - - -
14D GLY 3.4 16.1 + - - -
15D PRO 4.7 0.7 + - - +
117D TYR 3.0 12.7 + - - -
118D GLY 3.6 3.1 - - - -
119D PHE 3.1 0.2 - - - -
120D GLY* 1.3 72.8 - - - +
122D GLN* 1.3 63.0 + - - +
123D LEU 3.0 4.5 - - - -
124D LEU* 3.0 31.2 + - - +
125D HIS* 4.5 2.6 + - - -
138D LEU* 3.9 9.7 - - - +
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ALA 4.0 7.8 - - - +
15D PRO 2.7 27.4 - - - +
16D GLU* 3.3 11.9 + - - -
17D GLU* 3.0 22.8 + - + +
27D MSE 3.3 26.0 - - + -
70D LEU* 3.8 23.3 - - + +
74D LYS* 2.8 36.4 - - - +
118D GLY 3.2 9.1 + - - +
119D PHE 3.9 0.2 - - - +
121D SER* 1.3 78.5 - - - +
123D LEU* 1.3 57.3 + - - +
124D LEU 3.0 5.5 + - - -
125D HIS* 3.3 29.8 + - - +
126D PHE* 4.8 2.4 + - - -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.9 23.3 - - + -
70D LEU* 4.1 7.8 - - + +
86D VAL* 5.4 1.8 - - + -
88D LEU* 5.1 8.7 - - + -
89D PRO* 3.7 15.9 - - + -
92D TYR* 3.5 45.3 - - + -
119D PHE* 2.8 20.1 + - + +
120D GLY* 3.2 8.7 - - - +
121D SER 3.0 0.2 - - - -
122D GLN* 1.3 76.7 - - - +
124D LEU* 1.3 62.9 + - + +
125D HIS 3.4 0.7 - - - -
126D PHE* 3.8 36.8 + - + +
128D SER* 5.3 2.3 - - - -
131D ASN* 4.6 4.7 + - - -
134D ILE* 5.5 7.0 - - + +
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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