Contacts of the helix formed by residues 142 - 148 (chain A) in PDB entry 1LII
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.8 32.8 - - + +
22A ILE* 4.4 3.4 - - + -
46A LEU* 3.9 19.5 - - + -
125A GLY* 3.3 14.7 - - - -
140A THR* 3.9 9.7 + - + -
141A HIS* 1.3 74.5 - - - +
143A GLY* 1.3 68.0 + - - +
144A ALA 3.2 0.5 + - - -
145A CYS* 3.1 27.0 + - + -
146A GLY* 4.5 9.9 - - - +
172A THR* 3.6 36.8 - - + +
173A ALA* 5.3 0.7 - - + +
699A ADN 3.8 17.9 - - + +
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Residues in contact with GLY 143 (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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122A GLN* 3.5 17.4 + - - -
123A SER* 3.5 12.6 - - - -
125A GLY* 4.8 0.4 - - - -
141A HIS* 3.4 26.4 + - - -
142A LEU* 1.3 75.4 - - - +
144A ALA* 1.3 64.4 + - - -
145A CYS 3.1 1.4 + - - -
146A GLY* 3.2 12.3 + - - -
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Residues in contact with ALA 144 (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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93A ALA* 3.5 8.3 - - - +
94A ILE* 3.5 36.8 - - - +
95A GLY* 3.5 10.1 - - - +
119A ALA* 3.8 9.9 - - + -
122A GLN* 3.8 17.5 - - + +
123A SER 2.8 15.0 + - - +
124A THR* 4.6 1.6 - - - -
142A LEU 3.2 1.0 + - - -
143A GLY* 1.3 71.2 - - - -
145A CYS* 1.3 62.8 + - - +
147A SER* 2.9 21.4 + - - -
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Residues in contact with CYS 145 (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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20A ASN* 3.6 43.7 - - + +
21A PRO* 3.5 30.3 - - + -
22A ILE* 4.1 7.9 - - - -
93A ALA* 3.8 12.7 + - - +
125A GLY* 4.6 2.5 - - - -
142A LEU* 3.1 27.3 + - + +
144A ALA* 1.3 76.9 - - - +
146A GLY* 1.3 62.2 + - - +
147A SER 3.2 1.0 + - - -
148A PHE* 3.3 18.0 + - - +
173A ALA* 3.7 7.9 - - - +
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Residues in contact with GLY 146 (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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122A GLN* 6.1 0.2 - - - -
142A LEU* 4.4 11.1 + - - +
143A GLY 3.2 9.6 + - - -
144A ALA 3.0 2.2 + - - -
145A CYS* 1.3 79.8 - - - +
147A SER* 1.3 55.3 + - - +
148A PHE 3.3 1.6 - - - -
149A ARG* 3.2 18.7 + - - -
172A THR* 6.1 0.7 - - - -
173A ALA* 3.5 23.3 - - - +
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Residues in contact with SER 147 (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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93A ALA* 4.9 1.6 - - - -
117A MET* 3.6 11.1 - - - +
119A ALA* 4.2 11.9 - - - -
122A GLN* 2.7 29.9 + - - -
143A GLY 4.6 0.2 + - - -
144A ALA 2.9 11.6 + - - -
146A GLY* 1.3 76.4 - - - +
148A PHE* 1.3 66.1 + - - +
149A ARG* 3.3 23.1 + - - +
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Residues in contact with PHE 148 (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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18A ILE* 4.1 22.9 - - + -
19A GLY 4.9 6.3 - - - +
20A ASN* 5.8 1.1 - - - +
91A MET* 3.7 26.7 - - + -
92A GLY* 3.6 27.8 - - - -
93A ALA* 3.7 9.2 - - + +
115A ARG 5.3 1.3 - - - -
117A MET* 3.0 36.7 - - + +
145A CYS 3.3 15.9 + - - +
146A GLY 3.3 0.8 - - - -
147A SER* 1.3 79.1 - - - +
149A ARG* 1.3 86.6 + - - +
150A ILE* 4.0 20.6 - - + -
151A PRO* 4.7 4.3 - - + -
170A THR* 6.2 3.1 - - + -
173A ALA* 4.4 3.7 - - + +
177A ASN* 3.1 46.1 + - + +
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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