Contacts of the strand formed by residues 100 - 106 (chain T) in PDB entry 3HOU
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 100 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613M ILE* 6.2 6.7 - - + -
99T GLY* 1.3 73.8 - - - -
101T ALA* 1.3 85.2 + - - +
102T TYR* 3.7 4.4 + - + -
116T TYR* 3.2 7.4 - - - -
117T SER* 2.8 35.4 + - - +
136T LYS 5.4 0.2 - - - +
137T GLN 4.9 0.2 - - - -
138T GLU* 2.9 47.4 - - + +
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Residues in contact with ALA 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100T THR* 1.3 86.5 - - - +
102T TYR* 1.3 61.4 + - - +
104T PHE* 3.7 24.2 - - + -
115T TYR 3.0 9.9 - - - +
116T TYR* 3.3 32.2 - - + +
136T LYS 3.9 11.5 - - - +
137T GLN 4.0 13.6 + - - +
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Residues in contact with TYR 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597M LEU* 2.7 36.2 + - + -
598M LEU* 4.0 0.9 - - - -
606M LEU* 3.8 16.2 - - + -
608M ILE* 4.6 9.0 - - + +
613M ILE* 3.8 31.4 - - + -
614M PHE* 4.2 10.5 - + - -
100T THR* 3.9 3.8 - - + -
101T ALA* 1.3 74.4 - - - +
103T LYS* 1.3 70.4 + - + +
104T PHE* 5.0 1.9 - - - -
115T TYR* 2.9 28.3 + + + +
116T TYR 3.5 26.9 + - - -
117T SER* 3.5 17.3 - - - -
122T LEU* 3.1 30.3 - - + +
123T MET 5.0 0.2 + - - -
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Residues in contact with LYS 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597M LEU* 3.1 34.8 - - + +
102T TYR* 1.3 90.7 - - + +
104T PHE* 1.3 72.5 + - - +
105T GLU* 3.7 27.1 + - - +
114T VAL* 3.3 1.9 - - - -
115T TYR* 2.7 53.4 + - + +
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Residues in contact with PHE 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101T ALA* 3.7 22.4 - - + -
102T TYR 5.0 1.3 - - - -
103T LYS* 1.3 86.5 - - - +
105T GLU* 1.3 65.3 + - - +
106T GLU* 3.9 2.6 + - - +
112T ILE* 4.3 12.8 - - + +
113T ALA 3.5 5.4 - - - -
114T VAL* 3.4 26.9 - - + -
116T TYR* 5.0 1.6 - - - -
134T ASN* 3.1 26.5 - - + -
135T LEU 3.4 4.5 - - - -
136T LYS* 3.3 61.7 - - + -
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Residues in contact with GLU 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597M LEU* 4.1 9.2 - - - +
103T LYS* 3.7 28.9 + - - +
104T PHE* 1.3 75.6 - - - +
106T GLU* 1.3 63.5 + - - +
107T VAL* 3.7 4.0 - - - +
112T ILE* 2.8 24.0 - - - +
113T ALA* 2.8 24.6 + - + +
115T TYR* 3.0 39.1 + - + -
124T ARG* 3.0 22.7 + - - -
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Residues in contact with GLU 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T PHE 3.9 2.6 + - - +
105T GLU* 1.3 77.7 - - - +
107T VAL* 1.3 52.1 + - - +
108T SER* 2.3 27.5 + - - +
111T LEU 3.7 1.1 - - - -
112T ILE* 3.4 22.7 - - + -
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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