Contacts of the helix formed by residues 167 - 173 (chain A) in PDB entry 5IVI
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 LEU 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A SER* 3.1 20.4 + - - +
96A VAL 4.3 10.1 - - - +
97A GLN* 3.7 21.1 - - + +
134A HIS* 4.1 7.4 - - + +
138A PHE* 3.5 18.2 - - - +
139A ILE 3.9 9.0 - - - +
140A ILE* 3.5 32.1 - - - +
141A GLY 3.8 6.7 - - - +
165A TYR* 3.5 44.2 - - + +
166A ARG* 1.3 74.2 - - - +
168A GLY* 1.3 70.3 + - - +
170A LEU* 3.4 10.0 + - - +
171A GLY* 3.1 10.2 + - - -
172A PHE* 4.6 0.2 - - - -
291A ILE* 4.7 1.4 - - - +
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Residues in contact with GLY 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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96A VAL 5.7 0.2 - - - -
138A PHE 2.7 18.3 + - - -
139A ILE* 4.1 7.4 - - - +
167A LEU* 1.3 75.1 - - - +
169A ALA* 1.3 60.0 + - - -
171A GLY 3.0 1.4 + - - -
172A PHE* 2.8 31.6 + - - +
291A ILE* 4.7 4.0 - - - -
294A GLU* 3.5 19.5 - - - -
311A PHE* 4.2 6.7 - - - -
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Residues in contact with ALA 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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73A PHE* 3.6 6.7 - - + -
168A GLY* 1.3 71.3 - - - -
170A LEU* 1.3 63.1 + - + +
172A PHE 4.3 0.2 - - - +
173A LEU* 3.1 32.4 + - + +
263A LEU* 3.9 18.6 - - + -
290A LEU* 5.4 5.4 - - + -
291A ILE* 4.2 5.8 - - + +
294A GLU* 2.7 21.8 + - - +
311A PHE* 3.8 31.4 - - + -
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Residues in contact with LEU 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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72A ARG* 3.8 41.1 - - + +
73A PHE* 4.1 23.2 + - + -
95A SER* 5.7 2.2 - - - +
96A VAL* 3.9 34.5 - - + +
109A GLU* 3.9 16.6 - - + +
166A ARG* 3.8 29.0 + - + -
167A LEU 3.4 7.8 + - - +
168A GLY 3.1 0.8 - - - -
169A ALA* 1.3 79.3 - - + +
171A GLY* 1.3 57.9 + - - +
186A ALA* 4.7 0.5 - - - +
287A PRO* 4.1 10.8 - - + +
290A LEU* 5.0 9.6 - - + -
291A ILE* 4.3 15.2 - - + +
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Residues in contact with GLY 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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166A ARG* 3.5 30.9 - - - +
167A LEU 3.1 6.3 + - - -
168A GLY 3.0 5.6 + - - -
170A LEU* 1.3 78.2 - - - +
172A PHE* 1.3 65.2 + - - +
173A LEU 3.9 0.9 - - - -
186A ALA* 3.1 14.7 + - - +
187A GLY 2.9 23.9 + - - -
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Residues in contact with PHE 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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138A PHE* 3.7 39.5 - + + -
165A TYR* 4.8 2.9 - + - -
166A ARG 3.4 20.6 - - - -
168A GLY* 2.8 22.4 + - - +
169A ALA 4.0 0.4 - - - -
171A GLY* 1.3 94.5 - - - +
173A LEU* 1.3 67.9 + - - +
174A SER* 3.4 3.5 + - - -
184A GLY* 4.9 0.9 - - - -
185A ASN* 3.9 17.2 + - - +
187A GLY* 3.9 14.4 - - - -
188A LEU* 3.8 28.5 - - + -
256A CYS* 3.7 18.5 - - - -
311A PHE* 4.0 7.1 - - - -
312A GLY* 3.4 38.1 - - - +
313A PRO* 3.5 10.5 - - + -
314A THR* 5.6 0.2 - - - +
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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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73A PHE* 3.6 43.3 - - + +
169A ALA* 3.1 22.2 + - + +
171A GLY 3.9 0.6 - - - -
172A PHE* 1.3 78.9 - - - +
174A SER* 1.3 60.3 + - - +
175A LEU* 4.4 5.8 - - + -
182A VAL* 3.7 21.7 - - + +
184A GLY* 3.2 15.9 - - - -
186A ALA* 5.6 0.9 + - - +
260A ALA* 3.7 22.7 - - + -
263A LEU* 4.5 3.1 - - + -
279A LEU* 4.4 7.6 - - + -
282A LEU* 3.9 22.4 - - + -
311A PHE* 3.7 30.5 - - + -
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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