Contacts of the helix formed by residues 61 - 70 (chain B) in PDB entry 4LVB
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 GLY 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B TYR* 1.3 81.0 - - - +
62B LEU* 1.3 66.0 + - - +
63B GLN 3.2 2.7 - - - -
64B TYR* 3.3 21.1 + - - +
65B ILE* 3.6 11.7 + - - +
121B GLU* 2.9 11.3 + - - -
155B SER* 5.1 0.9 - - - -
158B PRO* 3.9 19.6 - - - +
231B TYR* 3.3 12.1 - - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE* 3.7 20.8 - - + -
60B TYR 3.7 2.2 - - - -
61B GLY* 1.3 76.2 - - - +
63B GLN* 1.3 58.7 + - - +
65B ILE* 3.0 15.2 + - + +
66B LEU* 2.9 43.4 + - + +
116B ILE* 4.2 11.0 - - + -
118B ALA* 3.8 28.9 - - + -
121B GLU* 3.0 7.9 + - - +
132B PHE* 4.2 17.3 - - + -
152B LEU* 3.6 31.0 - - + -
155B SER* 4.8 6.8 - - - -
461B VAL* 4.2 15.0 - - + -
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY 3.2 0.6 - - - -
62B LEU* 1.3 74.0 - - - +
64B TYR* 1.3 60.5 + - - +
66B LEU* 4.3 11.2 - - + -
67B ASN* 2.9 45.9 + - - +
121B GLU* 2.7 18.5 + - - +
230B TYR* 2.9 24.5 + - - +
231B TYR* 3.3 20.1 + - + +
467B VAL* 5.5 2.9 - - + -
469B LYS 4.5 1.4 - - - +
470B SER* 3.2 19.9 - - - -
471B TYR* 2.8 54.5 + - - +
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Residues in contact with TYR 64 (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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60B TYR* 6.4 0.2 - - + -
61B GLY* 3.3 11.6 + - - +
62B LEU 3.2 0.2 - - - -
63B GLN* 1.3 78.0 - - - +
65B ILE* 1.3 71.9 + - + +
67B ASN* 4.1 0.5 - - - +
68B LYS* 2.9 58.4 + - + +
69B TYR* 4.5 7.2 - + - -
158B PRO* 6.4 0.9 - - + -
202B GLU* 2.7 34.6 + - - +
206B ILE* 3.5 31.8 - - + +
226B LEU* 3.6 26.8 - - + +
230B TYR* 3.6 42.9 - + + -
231B TYR* 3.5 16.4 + - + +
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Residues in contact with ILE 65 (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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61B GLY 3.8 10.8 - - - +
62B LEU* 3.0 11.1 + - + +
64B TYR* 1.3 89.5 - - + +
66B LEU* 1.3 66.1 - - - +
69B TYR* 3.0 35.6 + - + +
70B LEU* 3.4 6.0 + - + +
151B ILE* 3.7 48.7 - - + +
152B LEU* 4.2 11.9 - - + +
154B GLN* 4.4 4.5 - - + -
155B SER* 3.9 34.5 - - - +
158B PRO* 5.6 1.6 - - + -
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Residues in contact with LEU 66 (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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62B LEU* 2.9 37.8 + - + +
63B GLN* 3.7 13.0 - - + +
65B ILE* 1.3 75.6 - - - +
67B ASN* 1.3 57.2 + - - +
70B LEU* 3.1 21.6 + - + +
71B LYS* 3.0 32.1 + - - +
116B ILE* 3.9 28.3 - - + -
461B VAL* 3.8 42.0 - - + +
462B PHE* 4.1 10.9 - - + -
467B VAL* 4.1 18.4 - - + -
469B LYS 5.4 0.9 - - - +
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Residues in contact with ASN 67 (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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63B GLN* 2.9 41.7 + - - +
66B LEU* 1.3 81.8 - - - +
68B LYS* 1.3 65.5 + - - +
71B LYS* 2.7 55.7 + - - +
230B TYR* 3.7 27.2 + - + -
467B VAL* 3.8 20.5 - - - +
470B SER* 5.9 1.0 - - - -
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Residues in contact with LYS 68 (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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9B PHE* 5.5 0.7 - - - +
64B TYR* 2.9 53.9 + - + +
67B ASN* 1.3 76.1 - - - +
69B TYR* 1.3 101.9 + - + +
202B GLU* 3.9 4.7 - - - -
229B LYS* 5.8 1.6 - - - +
230B TYR* 3.5 25.2 + - + +
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Residues in contact with TYR 69 (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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201A GLN* 3.5 24.0 - - + +
9B PHE* 3.5 61.1 - + + -
11B ILE* 4.1 7.3 - - - +
64B TYR* 4.5 6.5 - + - -
65B ILE* 3.0 30.4 + - + +
68B LYS* 1.3 117.8 - - + +
70B LEU* 1.3 73.2 + - + +
71B LYS 3.8 1.1 - - - -
74B VAL* 3.7 14.7 - - - +
151B ILE* 5.4 6.7 - - + -
154B GLN* 5.7 0.9 - - - -
202B GLU* 2.6 34.0 + - - -
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Residues in contact with LEU 70 (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 ILE* 3.5 27.6 - - + -
65B ILE* 3.4 8.0 + - + +
66B LEU* 3.1 26.5 + - + +
69B TYR* 1.3 82.5 - - + +
71B LYS* 1.3 64.9 + - - +
72B GLY 4.0 1.2 + - - +
74B VAL* 3.5 12.0 - - - +
112B LEU* 3.9 18.5 - - + +
116B ILE* 4.4 8.5 - - + -
148B ILE* 4.3 9.2 - - + -
151B ILE* 3.5 35.9 - - + -
152B LEU* 3.7 18.6 - - + -
462B PHE* 3.6 24.6 - - + -
465B GLY* 4.9 0.7 - - - -
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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