Contacts of the helix formed by residues 162 - 169 (chain A) in PDB entry 1L8F
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TRP* 3.7 40.8 - - + +
11A CYS* 5.1 0.2 - - - -
35A PHE* 3.9 12.3 - - + -
56A ALA* 3.9 17.5 - - + -
59A SER* 4.7 0.4 - - - +
124A PRO* 3.4 20.4 - - + +
138A PHE* 3.7 25.4 - - + -
141A LEU* 4.3 9.6 - - + -
158A PHE* 4.3 8.1 - - + -
159A PRO* 2.7 41.8 + - + +
161A PRO* 1.3 72.8 - - - +
163A LYS* 1.3 62.1 + - - -
164A PRO* 3.5 1.6 - - - -
165A GLY 3.7 3.2 + - - +
166A CYS* 3.2 22.4 + - - +
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Residues in contact with LYS 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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155A CYS* 3.5 18.8 - - + +
156A ASP* 3.2 38.1 + - - +
158A PHE* 3.5 20.4 - - + +
159A PRO 3.3 3.1 + - - +
160A GLU* 3.0 31.3 + - - +
162A LEU* 1.3 75.8 - - - +
164A PRO* 1.3 76.4 - - + +
166A CYS* 3.0 7.1 + - - +
167A GLN* 2.9 43.6 + - - +
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Residues in contact with PRO 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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59A SER* 6.1 0.7 - - - -
60A PRO 5.2 1.6 - - - +
160A GLU* 3.2 18.6 - - - +
161A PRO 3.8 8.1 - - - +
162A LEU 3.6 2.7 - - - -
163A LYS* 1.3 91.6 - - + +
165A GLY* 1.3 57.0 + - - +
167A GLN* 3.3 11.2 + - - +
168A TRP* 2.9 28.8 + - - +
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Residues in contact with GLY 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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59A SER* 4.1 18.7 - - - -
60A PRO* 4.2 6.3 + - - -
123A ILE* 3.6 13.2 - - - +
124A PRO* 3.7 20.8 - - - +
161A PRO 5.3 0.6 + - - -
162A LEU 3.7 3.6 + - - -
163A LYS 3.3 0.6 - - - -
164A PRO* 1.3 77.0 - - - +
166A CYS* 1.3 65.5 + - - +
168A TRP* 3.4 19.8 + - - +
169A ARG 3.5 3.6 + - - -
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Residues in contact with CYS 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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124A PRO* 3.4 18.4 - - - +
149A ILE* 3.4 21.3 - - - -
155A CYS* 2.0 51.1 - - + -
158A PHE* 3.6 18.6 - - + -
162A LEU 3.2 15.0 + - - +
163A LYS* 3.0 8.5 + - - +
165A GLY* 1.3 81.2 - - - +
167A GLN* 1.3 59.5 + - - +
169A ARG* 3.3 17.2 + - - +
170A PHE* 3.5 10.6 - - - -
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Residues in contact with GLN 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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152A ARG* 3.4 45.1 + - + +
155A CYS* 3.9 21.0 - - + +
156A ASP* 4.6 12.5 + - - -
163A LYS* 2.9 36.0 + - - +
164A PRO* 3.8 8.4 - - - +
166A CYS* 1.3 70.6 - - - +
168A TRP* 1.3 66.4 + - - +
169A ARG 3.0 2.7 - - - -
170A PHE* 2.9 8.8 + - - +
171A ASP* 2.9 29.8 + - - +
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Residues in contact with TRP 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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60A PRO* 3.3 26.9 - - + +
61A TRP* 3.7 20.6 - - - -
62A ALA* 3.8 6.1 - - + -
68A SER* 3.0 21.8 + - - -
103A MET* 3.6 31.4 - - + -
121A LEU* 4.8 1.1 - - + -
123A ILE* 3.6 29.2 - - + -
164A PRO 2.9 17.0 + - - +
165A GLY* 3.5 12.8 - - - +
166A CYS 3.3 0.2 - - - -
167A GLN* 1.3 76.0 - - - +
169A ARG* 1.3 77.6 + - + +
170A PHE 3.2 0.5 + - - -
171A ASP* 4.5 5.8 - - - +
172A TRP* 3.2 49.3 + + + +
173A PHE* 3.1 47.1 + + + -
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Residues in contact with ARG 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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7A ARG* 3.5 33.7 - - - +
123A ILE* 3.6 27.8 - - + -
124A PRO 5.3 0.9 - - - -
125A GLY 2.9 29.6 + - - -
126A GLY* 5.0 0.2 - - - -
147A GLY 3.4 5.7 + - - -
149A ILE* 2.8 33.2 + - - +
150A SER* 4.3 2.2 - - - +
165A GLY 3.5 0.8 + - - -
166A CYS 3.3 13.6 + - - +
167A GLN 3.0 0.6 - - - -
168A TRP* 1.3 90.5 - - - +
170A PHE* 1.3 64.9 + - + +
173A PHE* 3.1 25.0 - - + +
174A GLN 3.4 0.2 + - - -
175A ASN* 2.7 60.9 + - - +
176A ALA 5.6 0.4 + - - +
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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