Contacts of the helix formed by residues 161 - 170 (chain B) in PDB entry 3E2A
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 THR 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASN* 3.5 10.8 - - - +
121A LEU* 4.6 3.1 - - + -
70B VAL* 4.5 5.2 - - + -
72B HIS* 5.6 4.0 - - - +
78B LEU* 4.0 31.0 - - + -
81B VAL* 4.8 2.5 - - + +
157B ASN 3.3 11.8 + - - +
158B LEU* 2.9 29.7 + - + +
160B ARG* 1.3 78.0 - - - +
162B SER* 1.3 64.7 + - - +
163B ILE* 3.7 6.7 + - + +
164B VAL* 3.0 21.0 + - - +
165B LYS* 3.0 26.7 + - - +
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Residues in contact with SER 162 (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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112A ASP* 3.6 22.2 - - - +
114A GLY* 3.6 24.7 + - - -
115A LEU* 4.3 2.3 + - - +
117A ASN* 4.9 2.4 - - - +
118A ASN* 2.7 35.6 + - - -
160B ARG 3.6 1.8 + - - -
161B THR* 1.3 69.7 - - - +
163B ILE* 1.3 65.6 + - - +
165B LYS* 4.6 4.0 - - - +
166B SER* 2.8 35.7 + - - -
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Residues in contact with ILE 163 (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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115A LEU* 6.3 2.2 - - + -
118A ASN* 5.5 0.2 - - - +
78B LEU* 3.3 54.3 - - + +
81B VAL* 4.1 13.2 - - + -
82B GLN* 3.6 42.0 - - + +
85B VAL* 4.2 14.0 - - + +
86B ASP* 4.5 8.5 - - - +
161B THR* 3.1 4.2 - - - +
162B SER* 1.3 83.7 + - - +
164B VAL* 1.3 62.9 + - - +
166B SER* 3.8 4.3 - - - -
167B ALA* 3.0 22.9 + - - +
170B ARG* 5.0 0.3 + - - -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 4.1 19.7 - - + -
85B VAL* 4.9 1.1 - - + -
93B ILE* 4.5 1.3 - - + -
158B LEU* 3.4 25.6 - - + +
159B GLY* 4.1 3.6 - - - -
161B THR* 3.0 19.5 + - - +
163B ILE* 1.3 72.0 - - - +
165B LYS* 1.3 66.3 + - - +
167B ALA* 3.1 3.8 + - - +
168B TRP* 3.0 60.5 + - + -
174B LEU* 3.9 24.2 - - + -
176B LEU* 4.2 6.5 - - + -
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Residues in contact with LYS 165 (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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110A ASP 4.6 11.3 + - - -
112A ASP* 4.3 27.6 - - - +
117A ASN* 4.7 8.2 - - - +
231A SO4 4.9 11.3 + - - +
159B GLY 3.4 17.0 - - - +
160B ARG* 4.0 16.2 - - + +
161B THR 3.0 20.2 + - - +
162B SER* 4.0 2.7 - - - +
164B VAL* 1.3 75.7 - - - +
166B SER* 1.3 56.6 + - - +
168B TRP* 3.3 11.7 + - + +
169B GLU* 2.9 42.2 + - + +
198B ARG* 3.8 29.6 - - + +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 4.1 8.7 - - - -
162B SER 2.8 23.6 + - - -
163B ILE* 3.8 4.3 - - - -
165B LYS* 1.3 72.6 - - - +
167B ALA* 1.3 61.5 + - - +
169B GLU* 3.4 16.7 + - - +
170B ARG* 3.0 42.4 + - - +
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Residues in contact with ALA 167 (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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85B VAL* 3.7 25.4 - - + -
163B ILE 3.0 14.2 + - - +
164B VAL 3.1 8.5 + - - +
166B SER* 1.3 76.6 - - - +
168B TRP* 1.3 59.9 + - - +
170B ARG* 3.4 19.3 - - - +
171B GLY 3.4 3.3 + - - -
172B GLN* 2.9 38.1 + - + +
174B LEU* 4.3 11.9 - - + -
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Residues in contact with TRP 168 (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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159B GLY* 3.6 22.4 - - - -
164B VAL* 3.0 37.3 + - + -
165B LYS* 3.7 11.7 - - - +
167B ALA* 1.3 74.8 - - - +
169B GLU* 1.3 68.2 + - - +
171B GLY* 2.9 15.6 + - - -
172B GLN 4.0 15.3 - - - -
174B LEU* 3.0 30.5 + - + +
176B LEU* 3.8 27.6 - - + -
195B ALA* 3.9 9.6 - - + -
196B THR 3.3 14.3 + - - -
197B SER* 3.4 41.1 - - - -
198B ARG* 3.4 23.8 - - + +
201B LEU* 4.4 2.2 - - + -
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Residues in contact with GLU 169 (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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112A ASP* 3.4 32.9 - - - +
165B LYS* 2.9 37.8 + - + +
166B SER* 3.6 12.8 + - - +
167B ALA 3.4 0.2 - - - -
168B TRP* 1.3 73.9 - - - +
170B ARG* 1.3 59.4 + - + +
171B GLY* 3.3 3.1 + - - -
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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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85B VAL* 4.2 0.2 - - - +
86B ASP* 2.7 34.6 + - - +
89B LYS* 5.4 2.4 - - - +
163B ILE 5.0 0.6 + - - -
166B SER* 3.0 37.8 + - - +
167B ALA* 3.4 25.7 - - - +
168B TRP 3.1 1.2 - - - -
169B GLU* 1.3 78.2 - - + +
171B GLY* 1.3 57.1 + - - +
172B GLN* 3.3 30.6 + - + +
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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