Contacts of the helix formed by residues 153 - 158 (chain B) in PDB entry 3L6D
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 HIS 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B ASP 5.8 0.2 + - - -
67B PRO* 4.0 23.9 + - + +
68B ALA* 3.9 20.4 - - + +
96B THR* 3.4 37.9 + - + -
98B VAL* 5.4 1.3 - - + -
149B ALA 3.1 23.5 + - - +
150B PHE 3.4 2.7 - - - +
151B GLU 3.1 0.2 - - - -
152B GLN* 1.3 108.7 + - + +
154B ARG* 1.3 65.7 + - - +
155B ALA 3.3 2.7 - - - -
156B LEU* 3.2 21.7 + - + +
157B LEU* 3.0 33.2 + - + +
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Residues in contact with ARG 154 (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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150B PHE* 2.9 40.6 + - + +
151B GLU* 3.3 43.0 + - - +
152B GLN 3.5 0.8 - - - -
153B HIS* 1.3 77.2 - - - +
155B ALA* 1.3 58.0 + - - +
157B LEU* 3.2 6.7 + - - +
158B GLU* 2.8 59.0 + - - +
164B THR* 3.4 26.1 + - + +
165B VAL* 5.6 0.4 - - - +
166B PHE* 5.3 4.2 - - - +
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Residues in contact with ALA 155 (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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33B LYS* 5.3 2.4 + - - -
151B GLU 5.0 0.2 + - - -
152B GLN 5.2 1.9 + - - +
153B HIS 3.3 0.6 - - - -
154B ARG* 1.3 77.2 - - - +
156B LEU* 1.3 65.6 + - - +
158B GLU* 3.3 22.7 + - - +
159B GLY* 3.4 7.1 + - - -
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Residues in contact with LEU 156 (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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11B ASP* 4.2 11.9 - - + +
12B VAL* 4.0 36.1 - - + -
28B LEU* 4.0 14.8 - - + +
33B LYS* 4.0 35.1 - - + +
68B ALA* 4.3 17.0 - - + -
70B ILE* 5.5 1.3 - - + -
153B HIS* 3.2 24.4 + - + +
155B ALA* 1.3 78.6 - - - +
157B LEU* 1.3 69.1 + - + +
159B GLY* 2.9 21.8 + - - -
160B LEU* 4.1 0.7 + - - +
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Residues in contact with LEU 157 (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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70B ILE* 4.4 11.4 - - + -
98B VAL* 3.9 33.9 - - + -
100B TYR* 3.7 14.7 + - - +
123B VAL* 5.0 2.5 - - + -
141B SER* 5.2 2.9 + - - -
143B HIS* 3.8 34.2 - - + +
150B PHE* 4.3 17.5 - - + -
153B HIS* 3.0 24.9 + - + +
154B ARG* 3.8 5.2 - - - +
156B LEU* 1.3 80.8 - - + +
158B GLU* 1.3 57.4 + - - +
159B GLY 3.0 5.2 - - - -
160B LEU* 3.0 36.9 + - + +
161B ALA* 3.5 5.2 + - - +
164B THR* 5.9 2.7 - - + -
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Residues in contact with GLU 158 (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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135B GLY 5.5 0.7 - - - +
154B ARG* 2.8 54.4 + - - +
155B ALA* 3.6 18.4 - - - +
156B LEU 3.2 0.2 - - - -
157B LEU* 1.3 75.7 - - - +
159B GLY* 1.3 61.5 + - - +
160B LEU 3.2 0.2 - - - -
161B ALA 3.3 22.2 - - - +
162B GLY* 3.8 22.6 + - - +
164B THR* 3.9 18.3 + - + +
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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