Contacts of the strand formed by residues 105 - 111 (chain B) in PDB entry 5LOH
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 ASN 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B VAL* 3.5 32.2 - - + +
64B VAL 3.3 7.3 - - - +
65B LYS* 3.9 13.9 - - - +
66B LYS* 4.6 1.6 - - - -
102B SER* 2.8 33.9 + - - -
103B ALA 3.9 0.6 - - - -
104B ASN* 1.3 96.7 - - - +
106B VAL* 1.3 60.7 + - - +
107B TYR* 3.3 26.0 + - + -
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Residues in contact with VAL 106 (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 LYS 3.5 2.9 - - - +
63B VAL* 3.7 1.2 - - - -
64B VAL 2.9 34.0 + - - +
66B LYS* 3.6 24.2 - - + -
69B MET* 3.7 36.8 - - + -
99B SER* 4.3 13.2 - - - +
100B LEU 3.5 12.3 - - - +
101B GLN* 4.1 19.7 - - + +
105B ASN* 1.3 72.0 - - - +
107B TYR* 1.3 64.4 + - - +
108B LEU* 3.8 19.5 - - + +
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Residues in contact with TYR 107 (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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32B ILE* 3.9 31.9 - - + -
50B TYR* 4.1 11.2 - + - -
61B VAL* 3.7 24.5 - - + -
62B LYS 3.7 2.7 - - - -
63B VAL* 3.8 19.4 - - + +
98B TYR 3.7 1.2 - - - +
99B SER* 3.5 3.3 - - - -
100B LEU* 2.9 48.1 + - + +
102B SER* 3.6 20.0 + - - -
105B ASN* 3.3 44.4 + - + -
106B VAL* 1.3 74.3 - - - +
108B LEU* 1.3 61.6 + - - +
109B VAL* 3.9 3.5 + - + -
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Residues in contact with LEU 108 (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 ALA 3.4 4.0 - - - +
61B VAL* 3.3 3.4 - - - -
62B LYS* 2.9 46.1 + - + +
64B VAL* 3.6 29.4 - - + -
69B MET* 5.7 2.9 - - + -
96B LEU* 3.7 25.4 - - + -
98B TYR 3.8 4.5 - - - +
99B SER* 5.4 4.5 - - - +
106B VAL* 3.8 18.8 - - + +
107B TYR* 1.3 75.5 - - - +
109B VAL* 1.3 61.2 + - - +
110B MET* 3.4 10.4 - - + +
176B GLY* 5.0 4.9 - - - +
177B LEU* 3.8 25.1 - - + -
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Residues in contact with VAL 109 (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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35B PHE* 3.6 34.8 - - + -
59B TYR* 3.6 24.7 - - + -
60B ALA 3.9 2.2 - - - -
61B VAL* 4.3 17.3 - - + +
96B LEU* 3.6 3.1 - - - +
97B TYR* 2.9 27.0 + - + -
98B TYR* 3.1 28.1 + - + +
100B LEU* 3.9 29.8 - - + -
107B TYR* 4.5 3.6 - - + +
108B LEU* 1.3 70.8 - - - +
110B MET* 1.3 59.6 + - - +
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Residues in contact with MET 110 (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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49B VAL* 5.6 0.4 - - + -
59B TYR* 3.4 12.1 - - - +
60B ALA* 2.9 37.6 + - + +
61B VAL 4.7 0.2 - - - -
62B LYS* 3.8 17.5 - - + +
94B VAL* 3.9 16.8 - - + +
95B HIS 3.2 17.3 - - - +
96B LEU* 3.7 21.1 - - + -
97B TYR* 3.7 6.5 - - - -
108B LEU* 3.4 26.0 - - + +
109B VAL* 1.3 77.2 - - - +
111B GLU* 1.3 65.1 + - - +
173B THR* 4.6 3.4 - - - -
177B LEU* 6.0 1.1 - - - -
901B STU 3.8 42.2 - - + -
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Residues in contact with GLU 111 (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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58B LEU 4.9 3.1 - - - -
60B ALA* 3.3 2.8 - - - +
94B VAL* 3.4 12.2 - - + -
95B HIS* 2.7 41.9 + - - +
97B TYR* 3.6 24.5 - - + +
110B MET* 1.3 77.2 - - - +
112B TYR* 1.3 60.2 + - - +
113B LEU* 3.3 23.3 - - + +
171B LYS* 3.0 32.6 + - - -
901B STU 2.9 24.8 + - - -
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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