Contacts of the strand formed by residues 63 - 68 (chain D) in PDB entry 1LBH
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 LEU 63 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C GLN* 4.3 21.1 - - - +
62D LEU* 1.3 75.3 - - - +
64D ILE* 1.3 75.6 + - - +
93D SER* 3.0 48.0 - - - +
95D VAL* 3.8 19.1 - - + +
117D GLN 3.8 22.7 - - - +
118D ARG* 4.5 7.0 - - + +
119D VAL* 4.4 7.0 - - + -
120D SER* 2.7 44.4 + - - +
121D GLY 3.1 5.0 + - - -
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D LEU 5.1 0.9 - - - +
63D LEU* 1.3 79.7 - - - +
65D GLY* 1.3 71.7 + - - +
66D VAL* 3.8 8.2 + - + +
83D ILE* 5.1 1.1 - - + -
87D ALA* 4.0 17.5 - - + -
92D ALA* 4.4 10.5 - - + -
93D SER 2.7 15.1 + - - +
94D VAL* 3.5 5.9 - - + -
95D VAL* 3.1 25.6 + - - +
121D GLY* 4.2 4.3 - - - +
123D ILE* 4.0 12.8 - - + -
301D VAL* 3.3 35.4 - - + -
304D LEU* 3.3 29.8 - - + -
305D LEU* 4.5 10.8 - - + -
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Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 1.3 74.3 - - - +
66D VAL* 1.3 61.3 + - - +
95D VAL* 3.7 6.7 - - - -
114D LEU* 3.8 11.4 - - - -
119D VAL* 3.6 25.2 - - - +
121D GLY 3.1 14.1 + - - -
122D LEU* 3.3 5.0 + - - +
123D ILE 3.0 23.7 + - - -
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 4.2 8.5 - - + +
65D GLY* 1.3 76.4 - - - +
67D ALA* 1.3 63.2 + - - +
68D THR* 3.3 12.0 + - - -
79D ILE* 6.5 0.2 - - + -
80D VAL* 4.8 12.3 - - + -
83D ILE* 3.7 22.7 - - + -
94D VAL* 3.5 31.4 - - + -
95D VAL 3.0 11.4 + - - +
96D VAL* 3.6 8.7 - - + +
97D SER 2.8 26.3 + - - +
114D LEU* 3.6 3.7 - - - +
123D ILE* 3.5 19.7 - - + +
125D ASN* 5.5 4.5 - - + -
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLY 4.0 0.2 - - - -
66D VAL* 1.3 70.7 - - - +
68D THR* 1.3 58.3 - - - +
97D SER 3.5 6.3 - - - -
99D VAL* 4.8 5.2 - - + -
107D CYS 5.1 0.9 - - - +
110D ALA* 4.3 20.6 - - + -
111D VAL* 4.6 4.3 - - + -
114D LEU* 3.7 16.9 - - + +
122D LEU* 5.1 0.2 - - - +
123D ILE 2.8 12.1 + - - +
124D ILE* 3.5 25.5 - - + +
125D ASN 2.9 28.1 + - - +
126D TYR* 4.5 1.6 - - - +
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Residues in contact with THR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 3.3 7.6 + - - -
67D ALA* 1.3 73.6 - - - +
69D SER* 1.3 73.6 + - - +
71D LEU* 3.8 23.7 - - + +
76D PRO* 3.9 5.9 + - - +
80D VAL* 4.0 9.0 - - + +
96D VAL* 3.8 17.3 - - + -
97D SER 2.9 21.6 + - - +
98D MET* 3.7 15.9 - - + -
99D VAL* 3.1 28.4 + - - +
125D ASN* 3.4 24.9 + - - -
126D TYR* 4.8 0.2 - - - -
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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