Contacts of the helix formed by residues 165 - 176 (chain A) in PDB entry 4L8E
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 SER 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.4 17.5 - - - -
102A GLN* 3.7 35.5 - - - +
159A LEU 4.6 1.7 + - - -
163A GLU 4.0 2.9 + - - -
164A TYR* 1.3 75.9 - - - +
166A ILE* 1.3 65.4 + - - +
167A ALA* 3.1 24.1 + - - +
168A ASP* 2.9 23.8 + - - +
169A ILE* 3.1 19.1 + - - +
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Residues in contact with ILE 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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23A PHE* 3.9 34.1 - - + -
81A LEU* 4.0 35.3 - - + +
82A LEU* 4.2 3.1 - - - -
85A ALA* 4.0 12.3 - - + -
91A PHE* 2.9 25.0 + - + +
92A LEU* 4.1 27.1 - - + -
102A GLN* 5.7 2.0 - - + +
103A LEU* 4.6 2.0 - - + -
106A LEU* 3.9 30.1 - - + +
165A SER* 1.3 73.4 - - - +
167A ALA* 1.3 58.3 + - - +
169A ILE* 3.8 8.1 - - + +
170A ALA* 3.0 29.5 + - - +
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Residues in contact with ALA 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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102A GLN 3.5 22.7 - - - +
105A TRP* 4.0 19.1 - - + -
106A LEU* 4.0 11.9 - - - +
109A GLN* 5.1 0.3 - - - +
159A LEU* 4.0 15.7 - - + +
165A SER* 3.0 13.2 + - - +
166A ILE* 1.3 81.2 - - - +
168A ASP* 1.3 62.5 + - - +
170A ALA* 3.4 3.5 + - - +
171A VAL* 3.2 29.0 + - - +
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Residues in contact with ASP 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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158A TYR* 3.5 21.5 - - - +
159A LEU* 2.9 31.7 + - - +
163A GLU 3.8 0.3 - - - +
164A TYR* 3.5 20.6 - - + -
165A SER* 2.9 32.9 + - - +
167A ALA* 1.3 73.2 - - - +
169A ILE* 1.3 61.0 + - - +
171A VAL* 3.2 0.8 + - - -
172A TYR* 2.9 34.7 + - - +
194A TRP* 2.9 30.8 + - + +
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Residues in contact with ILE 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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19A LYS* 3.1 30.9 - - - +
22A LEU* 4.0 14.7 - - + +
23A PHE* 4.2 29.4 - - + +
26A GLU* 4.8 4.0 - - + -
81A LEU* 4.1 12.6 - - + -
91A PHE* 4.4 11.0 - - + -
164A TYR* 3.4 38.4 - - + +
165A SER 3.1 13.2 + - - +
166A ILE* 3.8 14.4 - - - +
167A ALA 3.3 0.2 - - - -
168A ASP* 1.3 74.9 - - - +
170A ALA* 1.3 57.9 + - - +
172A TYR* 4.9 0.2 - - - -
173A PRO* 2.9 27.7 - - - +
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.2 31.0 - - + +
81A LEU* 4.1 7.4 - - + -
106A LEU* 3.7 20.9 - - + -
109A GLN* 3.4 29.5 + - + +
166A ILE 3.0 17.9 + - - +
167A ALA* 3.6 5.4 - - - +
168A ASP 3.2 0.2 - - - -
169A ILE* 1.3 79.7 - - - +
171A VAL* 1.3 60.6 + - - +
173A PRO* 3.6 4.0 - - - +
174A TRP* 4.0 2.4 - - - -
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Residues in contact with VAL 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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108A TRP* 4.1 7.0 - - + -
109A GLN* 3.6 26.7 - - + -
113A PHE* 3.7 20.6 - - + -
149A LEU* 4.0 20.2 - - + -
159A LEU* 3.5 20.9 - - + -
167A ALA 3.2 16.8 + - - +
168A ASP 3.2 0.4 + - - +
170A ALA* 1.3 78.3 - - - +
172A TYR* 1.3 65.8 + - - +
174A TRP* 3.0 7.1 + - - +
175A ALA* 2.9 19.7 + - + -
194A TRP* 3.6 24.5 - - + -
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Residues in contact with TYR 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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22A LEU* 4.1 17.7 - - + -
164A TYR* 5.1 0.4 - - - +
168A ASP 2.9 17.5 + - - +
169A ILE* 4.4 1.3 - - - +
171A VAL* 1.3 77.3 - - - +
173A PRO* 1.3 66.1 - - + +
176A LYS* 2.9 53.3 + - + +
194A TRP* 3.8 10.5 - + + -
195A LEU* 3.6 41.1 - - + -
198A ILE* 3.4 35.0 - - + -
199A GLN* 3.8 20.3 + - - +
204A THR* 3.6 29.6 - - + +
208A TYR* 3.9 13.6 - + - -
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Residues in contact with PRO 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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15A PRO* 3.2 39.7 - - + +
18A TYR* 4.1 0.4 - - + -
19A LYS* 3.9 10.3 - - + +
22A LEU* 3.8 15.3 - - + -
169A ILE 2.9 29.2 - - - +
170A ALA 3.6 5.4 - - - +
171A VAL 3.5 3.1 - - - -
172A TYR* 1.3 86.2 - - + +
174A TRP* 1.3 57.2 + - + +
176A LYS* 3.9 5.6 - - + +
177A CYS* 3.4 21.8 - - - -
208A TYR* 3.3 27.9 + - - +
303A GSH 4.9 0.5 - - - +
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Residues in contact with TRP 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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15A PRO* 3.6 20.3 - - + +
16A ASN* 3.0 22.8 + - - -
19A LYS* 3.9 10.3 - - - -
109A GLN* 3.3 24.9 - - - +
113A PHE* 3.6 18.4 - - + -
114A GLY* 3.7 10.5 - - - -
117A LEU* 3.7 17.3 - - + -
118A GLY* 3.6 29.8 - - - -
121A HIS* 3.5 25.8 - + - -
146A TYR* 4.3 0.2 - - - -
170A ALA 4.0 2.2 - - - -
171A VAL 3.0 7.4 + - - +
173A PRO* 1.3 76.9 - - - +
175A ALA* 1.3 65.6 + - - +
176A LYS 3.2 0.2 - - - -
177A CYS* 3.1 6.9 + - - +
181A GLN* 3.0 31.9 + - - -
301A GSH 3.4 49.9 + - + -
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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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113A PHE* 3.7 13.4 - - + -
146A TYR* 3.3 22.8 + - + +
149A LEU* 4.6 2.9 - - + -
171A VAL* 2.9 16.7 + - + +
172A TYR 4.0 0.4 - - - +
174A TRP* 1.3 71.5 - - - +
176A LYS* 1.3 61.8 + - - +
177A CYS 3.0 5.4 - - - -
178A TYR* 3.1 23.7 + - - +
191A VAL* 4.8 0.9 - - + -
194A TRP* 3.9 15.0 - - + -
195A LEU* 3.8 22.9 - - + +
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Residues in contact with LYS 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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172A TYR* 2.9 43.1 + - + +
173A PRO 3.9 8.3 - - - +
174A TRP 3.2 0.2 - - - -
175A ALA* 1.3 74.9 - - - +
177A CYS* 1.3 58.4 + - - +
178A TYR* 3.3 17.2 + - - -
179A GLU* 4.9 1.2 + - - +
195A LEU* 3.8 9.7 - - + +
199A GLN* 6.2 1.3 - - - +
208A TYR* 3.6 45.6 - - + -
303A GSH 4.9 17.7 + - - +
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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