Contacts of the helix formed by residues 172 - 180 (chain A) in PDB entry 3LON
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 VAL 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.7 8.1 - - + -
96A PRO* 4.0 34.5 - - + -
97A CYS* 4.7 6.5 - - + +
150A ALA* 3.7 21.1 - - + +
151A VAL* 2.8 21.2 + - - +
152A GLY* 4.7 1.6 - - - +
170A ILE 3.6 0.8 + - - -
171A PRO* 1.3 71.1 - - - +
173A GLU* 1.3 79.6 + - - +
174A ASN 3.3 0.2 - - - -
175A LEU* 3.0 47.6 + - + +
176A GLU* 3.1 16.1 - - - +
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Residues in contact with GLU 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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97A CYS 5.6 1.0 - - - +
118A ARG* 4.4 10.5 + - - -
121A ASP* 3.9 11.2 - - - +
151A VAL 4.9 0.6 - - - +
171A PRO* 2.9 23.4 + - + +
172A VAL* 1.3 102.2 - - - +
174A ASN* 1.3 68.6 + - - +
175A LEU 3.1 1.0 + - - -
176A GLU* 3.1 21.6 + - - +
177A THR* 3.2 16.4 + - - +
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Residues in contact with ASN 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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80A GLN* 3.1 39.4 + - - +
82A LEU* 4.0 2.9 - - + -
170A ILE* 3.7 25.0 - - + +
171A PRO* 2.9 32.9 + - - +
173A GLU* 1.3 78.9 - - - +
175A LEU* 1.3 56.0 + - - +
177A THR* 3.5 5.2 + - - -
178A THR* 2.9 33.3 + - - -
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Residues in contact with LEU 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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48A ILE* 3.6 34.5 - - + -
53A TRP* 3.8 35.2 - - + +
82A LEU* 3.8 31.9 - - + -
153A LEU* 4.5 9.2 - - + -
170A ILE* 4.4 5.4 - - + +
171A PRO 4.0 11.4 - - - +
172A VAL* 3.0 30.9 + - + +
174A ASN* 1.3 74.0 - - - +
176A GLU* 1.3 68.7 + - - +
178A THR* 3.0 4.7 + - - -
179A MET* 3.0 29.5 + - + +
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Residues in contact with GLU 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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49A ASN* 6.3 0.4 - - - -
96A PRO* 4.6 14.1 - - - +
172A VAL* 3.1 32.5 - - - +
173A GLU* 3.1 11.1 + - - +
175A LEU* 1.3 81.3 - - - +
177A THR* 1.3 58.3 + - - +
179A MET* 3.3 23.8 + - + +
180A ARG* 2.9 49.2 + - - +
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Residues in contact with THR 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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77A ASN* 5.8 1.1 - - - +
80A GLN* 3.8 19.5 - - - +
173A GLU* 3.2 13.1 + - - +
174A ASN* 3.7 8.9 - - - -
176A GLU* 1.3 78.3 - - - +
178A THR* 1.3 58.6 + - - +
180A ARG* 3.3 26.8 + - + +
181A SER* 2.8 29.2 + - - +
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Residues in contact with THR 178 (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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53A TRP* 3.9 10.5 - - + -
75A TYR* 3.7 28.6 - - + +
76A THR 4.5 4.7 - - - +
77A ASN* 3.5 33.9 + - + +
80A GLN* 3.6 3.6 - - - +
82A LEU* 3.4 18.8 - - + +
174A ASN 2.9 23.6 + - - -
175A LEU 3.0 5.1 + - - -
177A THR* 1.3 76.8 - - - +
179A MET* 1.3 57.4 + - - +
181A SER* 3.0 29.5 + - - +
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Residues in contact with MET 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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49A ASN* 6.0 6.7 - - + +
51A VAL* 4.6 8.5 - - - -
53A TRP* 3.6 23.1 - - + +
75A TYR* 3.5 46.5 - - + +
175A LEU* 3.0 14.4 + - + +
176A GLU* 3.6 39.7 - - + +
178A THR* 1.3 71.7 - - - +
180A ARG* 1.3 61.0 + - - +
181A SER 3.1 11.3 + - - +
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Residues in contact with ARG 180 (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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176A GLU* 2.9 41.5 + - - +
177A THR* 3.5 32.2 + - - +
178A THR 3.3 0.2 - - - -
179A MET* 1.3 77.0 - - - +
181A SER* 1.3 59.3 + - - +
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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