Contacts of the helix formed by residues 169 - 178 (chain A) in PDB entry 4I0A
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LYS* 4.1 7.9 - - - +
168A ILE* 1.3 78.7 - - - +
170A ARG* 1.3 65.0 + - - +
171A GLN* 3.7 11.2 + - - +
172A GLU* 3.1 38.5 + - - +
173A ILE* 3.1 25.5 + - - +
202A LYS* 3.8 35.9 - - - +
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Residues in contact with ARG 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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169A THR* 1.3 74.0 - - - +
171A GLN* 1.3 57.6 + - - +
173A ILE* 3.4 1.6 + - - -
174A GLY* 2.9 25.3 + - - -
181A ARG* 3.5 41.9 + - + +
182A GLU* 4.7 5.7 + - - +
184A VAL* 3.5 29.1 - - + +
185A GLY* 3.5 28.0 + - - +
188A LEU* 4.6 9.8 - - + +
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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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169A THR* 3.2 9.3 + - - +
170A ARG* 1.3 79.9 - - - +
172A GLU* 1.3 59.7 + - - +
174A GLY 3.4 0.5 + - - -
175A GLN* 2.8 56.9 + - - +
181A ARG* 3.7 30.4 + - - +
302A CMP 3.4 33.6 + - - +
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Residues in contact with GLU 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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61A ILE* 4.0 6.9 - - + +
64A TYR* 3.0 22.5 + - - +
90A LYS* 3.9 19.1 - - - +
167A LYS* 4.9 3.5 - - - +
168A ILE* 3.3 27.5 - - + +
169A THR* 3.1 38.1 + - - +
171A GLN* 1.3 78.0 - - + +
173A ILE* 1.3 66.3 + - - +
175A GLN* 3.0 14.1 + - - +
176A ILE* 2.9 28.2 + - - +
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Residues in contact with ILE 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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144A ILE* 4.0 26.5 - - + -
147A THR* 5.1 4.7 - - + -
148A LEU* 4.0 20.9 - - + -
151A LEU* 4.9 4.7 - - + -
168A ILE* 3.7 30.7 - - + -
169A THR 3.1 12.6 + - - +
170A ARG 3.7 5.4 - - - +
172A GLU* 1.3 75.3 - - - +
174A GLY* 1.3 59.9 + - - +
176A ILE* 2.9 26.0 + - - +
177A VAL* 3.0 18.3 + - + +
184A VAL* 3.8 28.7 - - + -
188A LEU* 4.1 17.5 - - + -
204A ILE* 4.4 0.9 - - + -
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Residues in contact with GLY 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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170A ARG 2.9 13.6 + - - -
171A GLN 3.7 2.0 - - - -
173A ILE* 1.3 77.2 - - - +
175A GLN* 1.3 56.2 + - - +
177A VAL* 4.3 0.4 - - - -
178A GLY* 2.9 10.9 + - - -
179A CYS* 2.9 47.7 + - - +
184A VAL* 3.5 15.5 - - - +
302A CMP 3.2 7.3 - - - +
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Residues in contact with GLN 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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51A LEU* 4.2 6.1 - - - +
59A GLU* 3.2 48.8 - - - +
60A MET* 3.3 13.9 - - - +
61A ILE* 3.0 51.0 + - + +
171A GLN* 2.8 41.3 + - - +
172A GLU* 3.0 10.7 + - - +
174A GLY* 1.3 74.7 - - - +
176A ILE* 1.3 63.4 + - - +
178A GLY* 4.3 1.4 + - - -
302A CMP 3.6 17.3 + - - +
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Residues in contact with ILE 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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60A MET* 4.5 2.4 - - - +
61A ILE* 4.0 20.4 - - + +
64A TYR* 4.3 25.4 - - + +
131A LYS* 2.7 38.7 + - - +
135A LEU* 4.3 1.4 - - - +
147A THR* 3.7 39.0 - - + +
151A LEU* 4.5 11.7 - - + -
168A ILE* 4.8 0.7 - - + -
172A GLU 2.9 23.8 + - - +
173A ILE* 3.4 7.4 - - - +
175A GLN* 1.3 79.5 - - - +
177A VAL* 1.4 59.6 + - - +
303A GOL 3.4 12.6 - - - -
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Residues in contact with VAL 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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135A LEU* 3.5 6.9 - - - +
140A VAL* 4.2 6.1 - - + +
143A ARG* 3.2 56.1 + - + -
144A ILE* 3.7 20.6 - - + +
147A THR* 3.2 29.8 - - - +
173A ILE* 3.0 18.9 + - + +
176A ILE* 1.4 77.1 - - + +
178A GLY* 1.3 59.9 + - - +
179A CYS* 3.6 28.0 - - - +
303A GOL 4.2 6.7 - - - +
136B ALA* 5.0 0.4 - - - -
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Residues in contact with GLY 178 (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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60A MET* 5.7 0.2 - - - -
140A VAL* 4.8 4.4 - - - +
143A ARG* 4.5 5.4 + - - -
174A GLY 2.9 10.7 + - - -
175A GLN 4.3 2.8 + - - -
176A ILE 3.5 2.2 - - - -
177A VAL* 1.3 80.4 - - - +
179A CYS* 1.3 61.4 + - - +
302A CMP 3.3 43.2 + - - -
136B ALA* 4.0 12.3 - - - +
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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