Contacts of the helix formed by residues 115 - 124 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14J HIS* 6.4 0.7 - + - -
23L ASP* 3.9 12.6 - - + -
26L LEU* 4.0 13.8 - - + +
27L MSE 3.6 53.6 + - + +
30L GLU* 4.3 16.6 - - + -
92L TYR* 4.3 0.9 - - - -
113L GLY 2.9 3.1 + - - -
114L PRO* 1.3 93.0 - - + +
116L PHE* 1.3 65.0 + - - +
117L TYR 3.4 1.5 + - - -
118L GLY* 4.2 3.5 - - - +
119L PHE* 3.0 25.2 + - + +
169L ASP* 3.3 4.9 - - - -
170L GLU* 3.9 29.1 - - + +
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Residues in contact with PHE 116 (chain L).
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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91L ILE* 3.7 26.0 - - + -
92L TYR* 2.6 60.0 + + - -
100L PHE* 3.7 35.0 - + - -
109L LEU* 4.0 23.1 - - + -
112L MSE 4.7 0.9 - - - -
113L GLY 3.4 10.8 + - - +
115L HIS* 1.3 73.6 - - - +
117L TYR* 1.3 83.4 + + - +
120L GLY* 3.2 6.9 + - - -
137L SER* 5.3 2.5 - - - -
138L LEU* 3.8 18.1 - - + +
141L THR* 4.0 25.8 - - + -
169L ASP* 2.8 13.1 + - + +
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Residues in contact with TYR 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K LEU* 4.2 15.2 - - + +
13L LEU* 3.8 18.8 - - + -
109L LEU* 3.8 3.8 - - + +
115L HIS 3.5 0.6 - - - -
116L PHE* 1.3 94.0 - + - +
118L GLY* 1.3 61.1 + - - +
121L SER* 2.8 32.7 + - - -
138L LEU* 3.5 37.0 - - + +
141L THR* 3.7 10.4 + - - -
142L PHE* 3.6 28.8 - + + -
169L ASP* 3.6 28.0 + - + -
171L MSE 3.7 19.5 - - + -
172L GLU* 2.5 36.1 + - + -
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Residues in contact with GLY 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ALA* 3.8 22.6 - - - +
13L LEU* 3.9 9.7 - - - +
27L MSE 4.1 11.7 - - - -
115L HIS* 3.5 6.4 + - - +
117L TYR* 1.3 76.6 - - - +
119L PHE* 1.3 65.4 + - - +
121L SER* 3.7 2.6 - - - -
122L GLN* 2.9 24.8 + - - +
169L ASP* 5.1 0.4 + - - -
171L MSE 5.8 2.0 - - - +
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Residues in contact with PHE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L MSE 3.7 28.2 - - + +
30L GLU* 3.3 36.6 - - + -
31L LYS 3.2 22.2 - - - -
32L LEU* 3.9 23.6 - - + -
70L LEU* 3.9 25.6 - - + -
89L PRO* 4.1 9.9 - - + -
92L TYR* 3.5 21.1 - + - +
115L HIS* 3.0 21.2 + - + +
118L GLY* 1.3 71.3 - - - +
120L GLY* 1.3 53.5 + - - +
122L GLN* 2.6 10.0 + - - +
123L LEU* 2.5 46.1 + - + +
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Residues in contact with GLY 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L TYR* 3.4 30.7 + - - -
116L PHE 3.2 10.2 + - - -
117L TYR 3.9 0.2 - - - -
119L PHE* 1.3 77.9 - - - +
121L SER* 1.3 62.5 + - - +
123L LEU* 3.1 17.9 + - - +
124L LEU* 3.1 19.8 - - - +
134L ILE* 4.6 1.5 - - - +
138L LEU* 3.9 9.2 - - - -
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Residues in contact with SER 121 (chain L).
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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170K LEU* 4.8 1.6 - - - -
173K ASN* 3.5 18.4 + - - +
12L ALA 2.8 23.4 + - - -
13L LEU* 3.3 20.8 + - - -
14L GLY 3.6 3.8 + - - +
15L PRO 5.3 0.3 - - - +
117L TYR 2.8 22.5 + - - -
118L GLY 3.7 0.2 - - - -
120L GLY* 1.3 73.4 - - - +
122L GLN* 1.3 62.0 + - - +
124L LEU* 3.3 25.8 - - - +
125L HIS* 4.7 4.3 + - - -
138L LEU* 3.6 10.6 - - - +
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Residues in contact with GLN 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ALA* 2.7 37.1 - - - +
14L GLY 3.6 3.5 - - - +
15L PRO 2.9 9.3 + - - -
16L GLU* 3.8 12.3 + - - +
17L GLU* 4.0 21.7 + - + +
27L MSE 3.6 22.9 - - + -
70L LEU* 3.9 21.7 - - + +
74L LYS* 5.5 2.4 - - + +
118L GLY 2.9 14.3 + - - +
119L PHE 2.6 10.7 + - - +
121L SER* 1.3 70.4 - - - +
123L LEU* 1.3 56.5 + - - -
124L LEU 3.1 5.4 - - - -
125L HIS* 2.6 59.0 + - + +
126L PHE* 5.0 2.4 - - - -
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Residues in contact with LEU 123 (chain L).
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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32L LEU* 4.0 18.4 - - + -
70L LEU* 5.3 2.7 - - + -
86L VAL* 4.9 1.6 - - + -
88L LEU* 4.0 22.4 - - + +
89L PRO* 3.2 32.5 - - + -
92L TYR* 3.7 24.2 - - + -
119L PHE* 2.5 26.3 + - + +
120L GLY* 3.1 9.6 + - - +
122L GLN* 1.3 68.8 - - - +
124L LEU* 1.3 61.5 + - + +
125L HIS 3.1 6.3 + - - -
126L PHE* 3.3 42.0 + - + +
127L ASP 5.0 0.2 + - - -
128L SER* 5.6 1.7 + - - -
131L ASN* 4.8 2.3 + - - -
134L ILE* 5.4 3.4 - - + -
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K ASN* 3.7 42.8 - - - +
174K LEU* 4.0 17.3 - - + -
120L GLY 3.1 18.8 - - - +
121L SER* 3.3 18.2 - - - +
122L GLN 3.1 0.8 - - - -
123L LEU* 1.3 77.7 - - - +
125L HIS* 1.3 63.3 + - + +
126L PHE 3.1 1.8 + - - -
127L ASP* 3.2 7.6 + - - +
131L ASN* 3.1 43.7 - - + +
134L ILE* 4.0 25.8 - - + -
135L SER* 4.4 7.4 - - - +
138L LEU* 5.2 0.7 - - + -
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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