Contacts of the helix formed by residues 169 - 177 (chain A) in PDB entry 4U2M
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 3.7 21.6 - - + +
145A LEU* 3.6 26.6 - - + +
148A LEU* 3.9 5.8 - - + +
149A ARG* 3.7 20.6 - - + -
153A ILE 3.1 20.4 + - - -
154A LEU 3.4 26.0 - - - -
155A THR* 3.8 6.6 + - + -
156A ASP* 3.3 6.1 - - - +
157A VAL* 4.7 0.2 - - - -
168A ALA* 1.3 72.3 - - - +
170A LYS* 1.3 66.9 + - - +
171A THR* 4.2 11.4 - - + -
172A VAL* 3.0 23.3 + - + +
173A LEU* 3.2 13.8 + - - +
214A TYR* 2.7 29.3 + - - +
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Residues in contact with LYS 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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23A LEU* 3.7 25.4 - - + +
156A ASP* 2.9 47.9 + - - +
157A VAL* 3.8 12.3 - - + +
168A ALA 4.0 0.4 + - - -
169A HIS* 1.3 72.2 - - - +
171A THR* 1.3 56.9 + - - +
173A LEU* 3.2 5.4 + - - +
174A MET* 2.9 30.7 + - - +
184A PHE* 3.7 39.7 - - + -
190A CYS 2.9 26.1 + - - -
191A ASN* 4.3 3.6 - - - +
192A LEU 3.1 25.6 + - - -
193A SER* 5.1 0.2 - - - +
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Residues in contact with THR 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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14A LEU* 3.1 22.2 - - + +
17A GLN* 2.5 44.5 + - - -
23A LEU* 3.6 12.5 - - - +
38A HIS* 3.5 29.1 + - + -
40A ALA* 4.9 7.9 - - + -
41A VAL* 4.8 6.3 - - + -
145A LEU* 5.7 0.9 - - + -
156A ASP* 5.1 0.8 + - - -
169A HIS* 3.1 14.0 - - + -
170A LYS* 1.3 80.4 - - - +
172A VAL* 1.3 65.3 + - + +
175A ALA* 3.1 14.0 + - - +
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Residues in contact with VAL 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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10A VAL* 5.4 5.6 - - + -
14A LEU* 5.0 4.0 - - + -
142A LEU* 5.2 4.0 - - + -
145A LEU* 3.9 29.6 - - + -
169A HIS* 3.0 15.7 + - + +
171A THR* 1.3 81.2 - - + +
173A LEU* 1.3 66.3 + - - +
175A ALA* 3.1 15.1 + - - +
176A CYS* 3.2 19.6 + - - -
213A MET* 4.4 17.3 - - + +
214A TYR* 3.7 44.6 - - + +
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Residues in contact with LEU 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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157A VAL* 4.1 10.3 - - + -
159A ILE* 3.9 33.9 - - + -
168A ALA* 4.0 12.8 - - + -
169A HIS 3.2 9.6 + - - +
170A LYS 3.2 7.0 + - - +
172A VAL* 1.3 77.9 - - - +
174A MET* 1.3 61.5 + - - +
176A CYS* 3.2 1.9 + - - +
177A SER* 3.0 29.5 + - - -
180A PHE* 3.8 27.8 - - + -
184A PHE* 4.0 10.3 - - + -
206A PHE* 5.3 1.1 - - + -
210A LEU* 3.6 31.0 - - + -
213A MET* 3.6 17.5 - - + -
214A TYR* 5.0 2.5 - - + -
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Residues in contact with MET 174 (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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13A GLN* 4.6 3.8 - - - +
17A GLN* 3.7 33.7 - - + +
22A LEU* 4.2 13.5 - - + -
23A LEU* 3.7 17.9 - - + -
170A LYS 2.9 17.5 + - - +
171A THR 3.8 0.2 - - - +
173A LEU* 1.3 76.7 - - - +
175A ALA* 1.3 63.7 + - - +
176A CYS 3.2 0.3 + - - -
177A SER 3.8 10.4 + - - +
180A PHE* 4.2 0.9 - - - +
181A TYR* 3.9 40.2 - - + +
184A PHE* 3.7 33.0 - - + -
185A THR* 3.9 24.2 - - + -
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Residues in contact with ALA 175 (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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9A HIS* 4.1 9.9 + - - -
10A VAL* 4.4 20.2 - - + +
13A GLN* 3.5 45.9 - - + +
14A LEU* 4.6 2.7 - - + -
17A GLN* 3.6 5.6 - - - +
171A THR 3.1 16.1 + - - +
172A VAL* 3.4 12.1 - - - +
174A MET* 1.3 78.4 - - - +
176A CYS* 1.3 59.4 + - - +
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Residues in contact with CYS 176 (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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6A HIS* 3.7 29.2 - - + -
9A HIS* 5.7 3.1 - - - -
10A VAL* 3.9 14.1 - - - -
172A VAL* 3.2 20.1 + - - +
174A MET 3.2 0.2 - - - -
175A ALA* 1.3 80.6 - - - +
177A SER* 1.3 56.8 + - - +
212A PHE* 5.8 1.6 - - + -
213A MET* 3.6 40.4 - - + -
236A GLN 5.0 0.5 - - - +
237A MET* 3.5 21.3 - - - +
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Residues in contact with SER 177 (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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173A LEU 3.0 13.1 + - - +
174A MET 3.8 5.2 + - - +
175A ALA 3.8 1.4 - - - -
176A CYS* 1.3 79.5 - - - +
178A GLY* 1.3 57.9 + - - +
179A LEU* 3.2 2.8 + - - +
180A PHE* 3.1 32.3 + - - -
181A TYR* 3.0 26.7 + - - +
213A MET* 4.1 1.8 - - - -
235A LEU* 2.8 23.3 + - - +
236A GLN 4.8 0.4 - - - -
237A MET* 4.1 14.8 - - - -
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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