Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 1EIA
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 TYR 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLN* 3.1 29.9 - - - +
160A PRO* 1.3 69.4 - - - +
162A PRO* 1.3 62.8 - - + +
164A PHE* 3.1 20.4 + + - +
165A VAL* 2.8 52.7 + - + +
190A THR* 2.6 44.4 + - - +
194A ALA* 4.1 1.3 - - + -
198A CYS* 3.5 23.8 - - - -
202A MET* 4.1 3.7 - - - -
211A LEU* 4.3 1.2 - - + +
214A LYS* 3.6 18.4 - - + +
215A MET* 3.7 43.1 - - + -
218A CYS* 3.8 24.8 + - + +
221A ILE* 5.7 0.8 - - + +
222A GLY 5.1 1.2 - - - +
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Residues in contact with PRO 162 (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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160A PRO* 3.1 12.1 - - + -
161A TYR* 1.3 95.2 - - + +
163A GLU* 1.3 62.7 + - + +
165A VAL* 3.2 10.7 + - + +
166A ASP* 2.8 32.3 + - - +
215A MET* 4.5 25.1 - - + +
218A CYS 5.2 2.9 - - - +
219A ARG* 5.6 7.4 - - - +
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Residues in contact with GLU 163 (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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159A GLU* 4.0 13.8 - - - +
160A PRO* 2.7 52.8 + - + +
162A PRO* 1.3 73.2 - - + +
164A PHE* 1.3 62.3 + - - +
166A ASP* 3.1 18.6 + - - +
167A ARG* 3.2 18.5 + - + +
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Residues in contact with PHE 164 (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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153A ILE* 3.4 30.3 - - + -
154A ARG 3.9 2.9 - - - -
155A GLN* 3.3 41.7 - - + -
159A GLU* 3.6 17.8 + - - +
160A PRO 3.3 1.8 + - - +
161A TYR* 3.1 31.8 + + - +
163A GLU* 1.3 79.7 - - - +
165A VAL* 1.3 64.5 + - - +
166A ASP 3.1 0.2 + - - -
167A ARG* 3.2 12.0 + - - +
168A LEU* 3.0 32.6 + - + +
189A LEU 3.8 10.3 - - - -
190A THR* 4.3 5.6 - - - -
193A ASN* 3.5 24.5 - - + -
194A ALA* 3.8 17.3 - - - -
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Residues in contact with VAL 165 (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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161A TYR* 2.8 67.9 + - + +
162A PRO* 3.2 10.7 + - + +
164A PHE* 1.3 78.9 - - + +
166A ASP* 1.3 59.0 + - - +
168A LEU* 3.7 6.4 - - - +
169A LEU* 2.9 56.2 + - + +
190A THR* 4.6 5.4 - - + -
211A LEU* 3.8 23.8 - - + -
215A MET* 3.8 10.8 - - + -
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Residues in contact with ASP 166 (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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162A PRO* 2.8 22.9 + - - +
163A GLU* 3.5 9.5 - - - +
164A PHE 3.1 0.2 - - - -
165A VAL* 1.3 75.4 - - - +
167A ARG* 1.3 58.4 + - + +
169A LEU* 3.0 11.6 + - - +
170A SER* 2.6 38.7 + - - -
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Residues in contact with ARG 167 (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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153A ILE* 3.8 22.0 - - + +
154A ARG 2.5 35.2 + - - +
156A GLY 4.6 0.2 - - - +
159A GLU* 3.3 31.6 + - - -
163A GLU* 3.2 12.0 + - + +
164A PHE* 3.2 12.8 + - - +
166A ASP* 1.3 76.7 - - + +
168A LEU* 1.3 56.7 + - - +
170A SER* 3.3 7.5 + - - -
171A GLN* 2.9 30.7 + - - +
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Residues in contact with LEU 168 (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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150A ALA* 3.7 25.6 - - + +
153A ILE* 3.9 20.8 - - + +
164A PHE* 3.0 25.8 + - + +
165A VAL* 3.7 4.5 - - - +
167A ARG* 1.3 77.0 - - - +
169A LEU* 1.3 58.3 + - + +
171A GLN* 3.3 1.6 + - - +
172A ILE* 2.9 57.3 + - + +
186A THR* 4.7 1.1 - - - +
189A LEU* 3.5 45.1 - - + +
190A THR* 3.7 21.1 - - + +
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Residues in contact with LEU 169 (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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165A VAL* 2.9 47.0 + - + +
166A ASP* 3.7 10.1 - - - +
168A LEU* 1.3 74.7 - - + +
170A SER* 1.3 60.9 + - - +
172A ILE* 3.9 5.1 - - + +
173A LYS* 2.9 31.1 + - - +
186A THR* 3.6 34.3 - - + -
190A THR* 5.0 7.6 - - + -
211A LEU* 4.2 14.6 - - + -
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Residues in contact with SER 170 (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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166A ASP 2.6 23.0 + - - -
167A ARG* 3.3 8.5 - - - -
169A LEU* 1.3 69.2 - - - +
171A GLN* 1.3 67.1 + - - +
173A LYS* 3.1 10.2 + - - +
174A SER* 2.9 29.2 + - - -
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Residues in contact with GLN 171 (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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148A PRO 3.7 14.2 + - - +
149A LYS* 3.5 12.8 - - - +
150A ALA* 4.3 7.4 - - - +
153A ILE* 3.0 38.6 - - + -
167A ARG 2.9 7.4 + - - +
168A LEU 3.6 4.7 - - - +
170A SER* 1.3 75.6 + - - +
172A ILE* 1.3 65.2 + - - +
173A LYS 3.0 0.2 + - - -
174A SER* 2.9 38.0 + - - +
175A GLU* 2.7 32.6 - - - +
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Residues in contact with ILE 172 (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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150A ALA* 3.5 18.2 - - + -
168A LEU* 2.9 46.2 + - + +
169A LEU* 3.9 4.5 - - - +
171A GLN* 1.3 71.8 - - - +
173A LYS* 1.3 66.2 + - - +
175A GLU* 3.2 20.8 - - - +
176A GLY 3.9 0.5 + - - -
177A HIS* 3.6 10.5 + - + +
182A SER* 3.9 27.5 + - - +
185A LEU* 3.7 35.0 - - + -
186A THR* 3.5 28.3 - - + -
189A LEU* 4.3 0.7 - - + -
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Residues in contact with LYS 173 (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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169A LEU 2.9 20.0 + - - +
170A SER* 3.1 8.5 + - - +
172A ILE* 1.3 76.7 - - - +
174A SER* 1.3 55.4 + - - +
175A GLU 2.5 17.0 + - - -
176A GLY* 2.7 17.0 + - - -
177A HIS 4.8 0.2 + - - -
182A SER* 5.9 1.1 - - - -
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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