Contacts of the helix formed by residues 176 - 181 (chain A) in PDB entry 4LGD
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 ALA 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU* 5.0 10.8 - - - +
173A ASP 4.4 1.5 + - - +
174A THR* 5.0 0.2 - - - -
175A MET* 1.3 89.6 - - + +
177A LYS* 1.3 63.9 + - + +
179A ASN* 4.2 1.1 - - - +
180A THR* 3.2 24.6 + - - -
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Residues in contact with LYS 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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38A TYR* 6.1 0.2 - - - +
66A GLU* 5.2 18.6 - - + +
167A VAL* 3.3 44.9 - - - +
170A GLN* 2.7 49.7 + - - +
171A LEU* 4.5 0.5 - - - +
173A ASP* 4.5 18.3 + - + +
176A ALA* 1.3 81.0 - - + +
178A ARG* 1.3 56.3 + - - +
179A ASN 3.0 8.6 + - - -
180A THR* 3.9 15.3 - - + -
181A VAL* 3.7 20.4 + - + +
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN 4.1 0.2 + - - -
171A LEU* 3.0 23.5 + - - +
172A THR* 4.1 22.4 + - - +
173A ASP 4.1 6.7 + - - +
174A THR* 3.2 41.2 + - - +
175A MET* 3.7 2.0 - - - +
176A ALA 3.4 0.8 - - - -
177A LYS* 1.3 77.1 - - - +
179A ASN* 1.3 58.6 + - - +
181A VAL* 5.7 0.2 - - - -
182A ILE* 3.0 24.7 - - + +
224B ILE 5.2 0.2 - - - -
225B HIS* 3.2 50.3 - - - +
226B PRO* 4.2 10.8 - - + +
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Residues in contact with ASN 179 (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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175A MET* 2.9 22.3 + - - +
176A ALA 4.2 1.3 - - - +
177A LYS 3.0 1.0 + - - -
178A ARG* 1.3 80.6 - - - +
180A THR* 1.3 64.7 + - - +
181A VAL 3.3 1.6 - - - -
182A ILE* 3.5 15.2 + - - +
183A GLY 3.2 15.2 + - - -
179B ASN* 2.9 57.5 + - - +
180B THR* 5.1 0.4 - - - +
182B ILE* 5.5 0.9 - - - +
183B GLY* 5.2 6.9 + - - -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 6.1 1.6 - - - +
176A ALA 3.2 19.6 + - - +
177A LYS* 3.9 18.8 - - + -
179A ASN* 1.3 74.3 - - - +
181A VAL* 1.3 76.0 + - + +
183A GLY* 3.4 9.1 + - - -
184A THR* 3.9 11.1 + - - -
179B ASN* 6.2 0.2 - - - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLN* 3.7 29.2 - - + +
171A LEU* 3.6 26.2 - - + -
177A LYS* 3.7 21.5 + - + +
179A ASN 3.3 0.2 - - - -
180A THR* 1.3 88.0 - - + +
182A ILE* 1.3 67.2 + - + +
183A GLY 3.1 0.2 - - - -
184A THR* 3.2 24.0 + - - +
185A PRO* 3.9 2.6 - - - +
188A MET* 4.3 16.2 - - + +
198A TYR* 4.3 8.1 - - - +
227B MET* 5.8 0.2 - - + -
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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