Contacts of the helix formed by residues 169 - 180 (chain B) in PDB entry 3CEI
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 ALA 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B HIS* 2.8 23.7 + - + +
167B LYS 4.7 0.4 - - - -
168B ASN* 1.3 80.5 - - - +
170B ARG* 1.3 63.7 + - - +
171B PRO* 3.1 7.9 - - + -
172B VAL* 3.0 32.1 + - + +
173B TYR* 3.2 9.9 + - - +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TRP* 5.9 2.6 - - - -
113B ALA 2.8 36.5 + - - -
114B THR* 3.5 14.6 + - + +
116B LEU* 2.7 30.3 + - - +
118B GLY 3.6 19.2 + - - +
157B VAL* 3.7 27.4 + - + +
159B GLU* 5.3 3.2 - - - +
162B TYR* 3.0 47.4 + - + +
168B ASN 2.8 10.8 + - - +
169B ALA* 1.3 71.2 - - - +
171B PRO* 1.3 66.0 - - + +
173B TYR* 3.0 11.2 + - + +
174B LEU* 2.7 44.1 + - + +
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Residues in contact with PRO 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 5.7 2.1 - - + +
114B THR* 4.5 22.2 - - + +
168B ASN 4.4 2.2 - - - +
169B ALA* 3.2 8.5 - - + -
170B ARG* 1.3 95.2 - - + +
172B VAL* 1.3 64.7 + - + +
174B LEU* 3.1 11.4 + - + +
175B GLU* 2.9 24.4 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B HIS* 3.8 21.5 - - + +
169B ALA* 3.0 25.0 + - + +
171B PRO* 1.3 77.8 - - + +
173B TYR* 1.3 62.7 + - - +
175B GLU* 3.3 7.5 + - + +
176B LYS* 3.0 35.5 + - + +
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.4 26.2 - + - -
18B LEU* 4.6 2.7 - - + -
76B TYR* 2.6 29.0 + - - -
155B VAL* 3.7 18.3 - - + +
156B ASP 2.8 29.2 + - - -
157B VAL* 4.7 1.3 - - + -
161B ALA* 3.7 19.9 - - + +
162B TYR* 3.3 39.7 - + + -
166B HIS* 3.8 23.7 + + + -
169B ALA 3.2 5.8 + - - +
170B ARG* 3.0 13.1 + - + +
172B VAL* 1.3 80.2 - - - +
174B LEU* 1.3 67.8 + - + +
176B LYS* 3.3 3.7 + - - +
177B PHE* 2.9 27.4 + - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 5.8 1.3 - - + -
110B ILE* 3.9 20.7 - - + +
113B ALA* 3.7 24.5 - - + +
114B THR* 3.3 43.5 - - - +
155B VAL* 3.9 26.9 - - + -
157B VAL* 4.2 5.2 - - + -
170B ARG* 2.7 32.9 + - + +
171B PRO* 3.6 5.4 - - + +
173B TYR* 1.3 83.1 - - + +
175B GLU* 1.3 56.3 + - - +
177B PHE* 3.1 7.9 + - + +
178B TYR* 2.9 30.7 + - - +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 2.9 37.6 + - - -
110B ILE* 3.8 12.6 - - + +
171B PRO 2.9 16.1 + - - +
172B VAL* 3.6 7.2 - - - +
174B LEU* 1.3 76.7 - - - +
176B LYS* 1.3 66.9 + - + +
178B TYR* 3.5 1.7 + - - +
179B GLY* 3.3 17.5 + - - -
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Residues in contact with LYS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP* 3.2 42.9 + - - +
17B PHE* 3.6 26.2 - - + -
166B HIS* 4.5 4.9 - - + -
172B VAL* 3.0 34.7 + - + +
173B TYR* 3.7 1.8 - - - +
175B GLU* 1.3 78.4 - - + +
177B PHE* 1.3 67.3 + - - +
179B GLY* 3.4 8.8 + - - -
180B HIS* 3.4 20.3 - - - -
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Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.6 21.5 - + + -
76B TYR* 4.0 7.4 - + - -
79B CYS* 4.8 3.8 - - + -
80B LEU* 3.5 31.0 - - + -
109B PHE* 4.0 15.9 - + - -
110B ILE* 6.5 0.4 - - + -
153B LEU* 3.9 9.9 - - + -
154B VAL 3.4 26.9 - - - -
155B VAL* 3.6 34.5 - - + -
173B TYR* 2.9 15.8 + - + +
174B LEU* 3.3 13.5 - - + +
176B LYS* 1.3 73.4 - - - +
178B TYR* 1.3 72.8 + + + +
180B HIS* 2.7 27.2 + - - +
181B ILE* 3.3 36.7 + - + +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU 4.5 2.1 + - - -
105B PHE* 3.2 27.9 - + - -
106B LYS* 3.5 53.8 - - + +
109B PHE* 4.2 20.9 - + + -
110B ILE* 4.1 22.2 - - + -
174B LEU 2.9 15.7 + - - +
175B GLU 3.7 5.2 - - - +
176B LYS 3.4 0.2 - - - -
177B PHE* 1.3 77.1 - + - +
179B GLY* 1.3 62.7 + - - +
180B HIS 3.1 1.2 + - - -
181B ILE* 3.2 35.4 + - + +
183B TRP* 3.4 31.7 + + - -
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA* 5.0 14.4 + - - +
175B GLU* 3.3 10.4 + - - -
176B LYS* 3.4 4.9 + - - -
177B PHE 3.1 1.4 - - - -
178B TYR* 1.3 77.6 - - - +
180B HIS* 1.3 65.9 + - - +
181B ILE 3.5 1.5 + - - +
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Residues in contact with HIS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER 4.9 0.9 - - - -
14B MET* 3.8 21.9 - - + +
16B ASP* 2.7 34.1 + - - -
17B PHE* 3.6 27.7 - + + +
80B LEU* 3.5 8.5 - - + -
81B SER* 2.8 54.5 + - - +
82B PRO 3.4 18.4 + - - -
83B LYS 5.7 1.7 - - - -
84B ALA* 6.3 0.7 - - - +
176B LYS 3.4 19.7 + - - +
177B PHE 2.7 16.3 + - - +
179B GLY* 1.3 76.8 + - - -
181B ILE* 1.3 60.1 + - - -
182B ASN 3.3 0.2 + - - -
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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