Contacts of the strand formed by residues 131 - 136 (chain E) 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 131 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ILE* 6.0 0.2 - - - +
106E GLN* 2.8 15.1 + - - +
107E THR* 3.5 3.8 + - - +
108E GLY 3.0 21.7 + - - -
124E VAL 5.5 1.8 - - - -
128E PRO* 6.0 0.4 - - + -
129E PRO 3.4 15.0 - - - +
130E ALA* 1.3 73.6 - - - +
132E ILE* 1.3 67.0 + - - +
133E GLU* 5.4 5.5 + - - +
191E LYS* 3.0 34.2 + - - +
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Residues in contact with ILE 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E MET* 5.4 1.3 - - - -
96E PHE* 3.7 22.2 - - + -
97E VAL* 3.8 29.2 - - + -
100E ILE* 4.3 13.7 - - + -
108E GLY 3.0 17.3 - - - +
110E PHE* 4.9 2.7 - - + -
124E VAL* 3.2 54.3 + - + +
127E ILE* 4.1 20.4 - - + -
131E THR* 1.3 80.4 - - - +
133E GLU* 1.3 72.2 + - - +
134E THR* 4.5 0.8 + - - -
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Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ARG* 2.4 49.0 + - - -
107E THR* 4.5 9.6 + - + +
108E GLY 2.7 12.1 + - - +
109E ILE* 3.3 10.3 - - + -
110E PHE* 2.8 28.8 + - - +
131E THR* 5.4 6.1 + - - +
132E ILE* 1.3 83.6 - - - +
134E THR* 1.3 59.5 + - - +
135E PHE* 3.1 20.8 - - + -
186E LEU* 4.0 3.8 - - - +
189E GLY* 4.0 11.2 - - - -
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Residues in contact with THR 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PHE* 3.7 7.1 + - - -
112E TYR* 3.1 30.1 - - + -
116E ILE* 4.0 11.0 - - - +
121E MET* 4.9 17.3 - - + -
124E VAL* 6.3 4.5 - - + -
132E ILE* 4.5 0.9 + - - -
133E GLU* 1.3 71.9 - - - +
135E PHE* 1.3 77.1 + - - +
186E LEU* 6.1 0.5 - - - +
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Residues in contact with PHE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E MET* 3.9 23.1 - - + -
26E ARG* 3.5 13.0 - - - -
109E ILE* 4.4 9.4 - - + -
110E PHE 3.2 8.5 + - - +
111E VAL* 3.4 9.0 - - + -
112E TYR* 3.0 33.1 + - - -
133E GLU* 3.1 39.5 - - + -
134E THR* 1.3 100.5 + - - +
136E ASN* 1.3 60.1 + - - +
139E ALA* 6.1 0.4 - - + -
140E LEU* 3.2 39.0 - - + -
186E LEU* 4.1 28.3 - - + -
187E TYR* 5.0 1.6 - + - -
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Residues in contact with ASN 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E VAL* 4.4 1.1 - - - -
112E TYR* 3.1 38.7 + - - +
113E GLN 3.7 9.5 + - - +
114E ASN* 5.2 1.8 - - - +
135E PHE* 1.3 74.3 - - - +
137E GLU* 1.3 64.9 + - - +
138E ALA* 2.4 43.4 + - - +
139E ALA* 3.0 24.0 + - + +
140E LEU* 3.1 20.4 - - - +
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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