Contacts of the strand formed by residues 106 - 109 (chain L) in PDB entry 6AHU
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 THR 106 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95L LEU* 4.7 4.0 - - + -
96L THR* 3.4 17.7 - - - +
99L THR 2.8 25.1 + - - +
100L HIS 3.3 13.3 + - - -
101L ILE* 3.9 16.8 - - + -
104L ASP 3.7 1.1 + - - -
105L ASN* 1.3 75.2 - - - +
107L VAL* 1.3 61.7 + - - +
108L ALA 4.2 0.3 + - - -
117L LEU* 3.5 0.3 - - - -
118L SER* 2.6 45.2 + - - +
143L LYS* 6.0 0.2 - - - -
319L ASP* 4.3 9.2 - - - +
321L PRO* 3.7 25.0 - - + +
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Residues in contact with VAL 107 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74L LEU* 3.8 31.2 - - + -
77L LEU* 5.5 0.2 - - + -
94L ALA* 3.9 2.2 - - + +
95L LEU* 3.8 4.9 - - - +
96L THR* 3.4 37.6 + - + +
106L THR* 1.3 77.9 - - - +
108L ALA* 1.3 63.9 + - - +
115L LEU* 3.8 23.3 - - + -
117L LEU* 3.7 35.7 - - + -
119L LEU* 5.1 2.2 - - + -
177L PHE* 3.9 20.6 - - + -
179L PHE* 4.5 7.5 - - + -
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Residues in contact with ALA 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L TYR* 3.4 17.3 - - + +
94L ALA* 3.4 6.3 - - - +
95L LEU* 4.6 0.9 - - + -
106L THR 4.2 0.2 + - - -
107L VAL* 1.3 75.4 - - - +
109L LEU* 1.3 60.6 + - - +
110L LEU* 5.0 5.6 - - + -
115L LEU* 3.4 11.4 - - - +
116L ILE* 2.9 39.5 + - + +
117L LEU* 4.2 0.2 - - - +
321L PRO* 3.8 30.1 - - + -
322L VAL* 5.5 2.5 - - + +
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Residues in contact with LEU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L TYR* 5.7 1.2 - - - +
38L TYR* 3.0 18.1 + - - -
77L LEU* 5.8 3.8 - - + -
82L PHE* 4.8 7.4 - - + -
87L ILE* 4.7 15.3 - - + -
92L CYS* 3.5 37.2 - - + +
93L TYR* 4.2 8.7 - - - -
94L ALA* 3.1 36.8 + - + +
108L ALA* 1.3 73.9 - - - +
110L LEU* 1.3 72.1 + - - +
111L PRO* 4.7 0.3 - - - +
113L GLY* 4.8 2.2 - - - -
114L LYS 4.2 3.4 - - - +
115L LEU* 3.8 35.4 - - + +
150L LEU* 4.3 13.7 - - + -
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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