Contacts of the helix formed by residues 148 - 152 (chain B) in PDB entry 5LMQ
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 TYR 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1098A C 3.7 20.8 + - - -
1099A G 2.9 21.9 + - - -
1103A C 5.9 0.9 - - - -
92B TYR* 4.9 0.5 - - - +
93B VAL* 4.4 20.6 - - - +
94B ASN 4.9 1.9 + - - -
95B GLN* 3.1 18.4 + - + +
96B ARG* 3.4 44.0 - - + +
98B LEU* 3.8 25.4 - - + -
101B MET* 4.6 5.5 - - - +
144B ARG* 3.1 32.1 - - + +
145B LEU 3.2 0.8 + - - -
147B LYS* 1.3 105.3 - - + +
149B LEU* 1.3 72.5 + - + +
150B SER* 3.2 7.5 + - - -
151B GLY 4.5 3.6 + - - -
152B PHE* 4.9 1.0 - - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103A C 5.9 0.4 - - - +
1104A G 5.0 6.7 - - - +
98B LEU* 4.3 15.0 - - + -
108B ILE* 3.7 24.5 - - + +
111B ARG* 3.7 29.6 - - + -
112B VAL* 3.8 15.5 - - + +
115B LEU* 4.3 9.3 - - + +
144B ARG 4.9 0.4 - - - +
145B LEU* 2.7 43.8 + - + +
148B TYR* 1.3 84.7 - - + +
150B SER* 1.3 57.8 + - - +
151B GLY 3.3 2.5 - - - -
152B PHE* 3.0 28.2 + - + -
153B ARG* 3.5 17.3 + - - +
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Residues in contact with SER 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 4.3 5.2 + - - -
92B TYR* 2.7 38.6 + - - -
94B ASN* 5.6 1.4 - - - +
145B LEU 3.6 2.6 + - - -
146B GLN 3.3 27.1 - - - -
147B LYS 4.8 5.2 - - - -
148B TYR 3.2 1.9 - - - -
149B LEU* 1.3 76.4 - - - +
151B GLY* 1.3 57.4 + - - +
152B PHE 3.3 0.6 + - - -
153B ARG* 3.3 34.7 + - - +
154B LEU* 4.0 7.3 - - - +
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.6 0.2 - - - +
91B PRO* 3.3 14.0 - - - +
92B TYR* 2.8 65.9 + - - +
148B TYR 4.5 2.2 + - - -
149B LEU* 3.3 0.6 - - - +
150B SER* 1.3 79.2 + - - +
152B PHE* 1.3 55.0 + - - +
154B LEU* 3.4 10.5 - - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.1 17.7 - - + -
91B PRO* 5.3 1.3 - - - -
92B TYR 4.1 9.6 - - - +
101B MET* 3.4 68.6 - - + -
105B PHE* 3.7 24.0 - + - -
108B ILE* 3.8 21.3 - - + -
109B SER* 5.7 0.4 - - - -
112B VAL* 3.4 17.9 - - + +
148B TYR 4.9 0.7 - - - +
149B LEU* 3.0 31.3 + - + +
151B GLY* 1.3 77.8 - - - +
153B ARG* 1.3 58.5 + - - +
154B LEU 3.2 8.2 + - - -
155B LEU* 3.8 22.9 + - + +
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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