Contacts of the helix formed by residues 82 - 91 (chain B) in PDB entry 2LYL
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 SER 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ARG* 4.3 1.8 - - - +
80B LYS 3.6 2.2 + - - -
81B ILE* 1.3 74.4 - - - +
83B GLN* 1.3 52.9 + - - +
84B SER* 3.1 28.4 + - - -
85B GLU* 2.5 34.7 + - - +
86B LEU* 2.6 30.5 - - - +
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Residues in contact with GLN 83 (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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72B LEU* 4.2 6.3 - - - +
73B LYS* 4.7 1.6 - - - +
76B ARG* 3.5 41.8 + - - +
82B SER* 1.3 73.8 + - - +
84B SER* 1.3 62.3 + - - +
86B LEU* 3.2 15.7 - - - +
87B ALA* 3.2 19.2 - - - +
94B ARG* 3.6 25.3 - - + +
97B ILE* 4.3 4.9 + - + +
98B ASN* 3.9 13.7 - - + +
101B GLU* 2.5 43.3 + - - +
102B LYS* 4.3 2.3 + - - -
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Residues in contact with SER 84 (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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82B SER* 3.1 12.5 + - - -
83B GLN* 1.3 79.9 + - - +
85B GLU* 1.3 58.0 + - - +
87B ALA* 3.6 2.4 - - - +
88B ALA* 3.0 27.9 + - - +
94B ARG* 2.3 47.5 + - - +
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Residues in contact with GLU 85 (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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80B LYS 4.2 2.4 - - - +
81B ILE* 3.4 22.9 - - + +
82B SER* 2.5 42.4 + - - +
84B SER* 1.3 76.0 - - - +
86B LEU* 1.3 79.3 + - + +
88B ALA* 2.9 10.3 + - - +
89B LEU* 2.9 31.0 + - + +
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Residues in contact with LEU 86 (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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72B LEU* 5.6 6.7 - - + -
76B ARG* 5.0 4.0 - - + -
81B ILE* 3.6 17.3 - - + -
82B SER 2.6 31.6 - - - +
83B GLN* 3.2 13.7 - - - +
85B GLU* 1.3 75.0 - - + +
87B ALA* 1.3 68.0 + - - +
89B LEU* 2.7 15.3 + - + +
90B LEU* 2.5 59.6 + - + +
97B ILE* 3.5 22.9 - - + -
115B ILE* 5.2 7.2 - - + +
118B TYR* 4.7 15.5 - - + +
119B LEU* 4.9 15.5 - - + +
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Residues in contact with ALA 87 (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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83B GLN 3.2 18.8 + - - +
84B SER 3.6 4.9 - - - +
85B GLU 3.2 0.2 - - - -
86B LEU* 1.3 86.2 - - - +
88B ALA* 1.3 50.9 + - - +
90B LEU* 3.1 3.7 + - - -
91B GLU 2.5 30.7 + - - -
92B VAL 2.7 28.0 + - - +
94B ARG* 3.8 12.8 - - - +
97B ILE* 3.5 22.2 - - + -
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Residues in contact with ALA 88 (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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84B SER 3.0 13.3 + - - +
85B GLU* 2.9 13.5 + - - +
87B ALA* 1.3 74.4 - - - +
89B LEU* 1.3 62.6 + - + +
91B GLU* 2.9 25.8 + - - +
92B VAL 3.9 2.0 + - - -
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Residues in contact with LEU 89 (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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85B GLU* 2.9 23.8 + - + +
86B LEU* 2.7 20.8 + - + +
88B ALA* 1.3 77.1 - - + +
90B LEU* 1.3 60.0 + - - +
91B GLU* 3.3 10.2 + - - +
118B TYR* 3.0 72.8 + - + +
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Residues in contact with LEU 90 (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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66A GLU 5.3 1.2 - - - +
86B LEU* 2.5 44.2 + - + +
87B ALA 3.3 6.7 - - - +
89B LEU* 1.3 72.0 - - - +
91B GLU* 1.3 71.9 + - - +
92B VAL* 3.5 10.7 - - + +
97B ILE* 3.5 17.9 - - + -
111B LEU* 3.8 21.3 - - + +
114B LYS* 3.3 26.2 - - + +
115B ILE* 3.3 53.8 - - + +
118B TYR* 4.1 7.2 - - + -
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Residues in contact with GLU 91 (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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65A PRO 3.9 17.7 - - - +
66A GLU* 5.5 0.9 - - - -
87B ALA 2.5 10.4 + - - -
88B ALA* 2.9 20.3 + - - +
89B LEU 3.5 8.1 - - - +
90B LEU* 1.3 81.2 - - - +
92B VAL* 1.3 60.3 + - - +
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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