Contacts of the helix formed by residues 132 - 142 (chain A) in PDB entry 5JTO
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 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ASN* 5.1 9.0 + - - +
130A PRO* 3.9 3.4 + - - +
131A VAL* 1.3 68.6 - - - +
133A PHE* 1.3 63.8 + - - +
134A ASP* 3.2 26.3 + - - +
135A ALA* 3.2 30.9 + - - +
136A LEU* 3.3 20.8 - - - +
145C ALA* 5.6 3.2 - - - +
146C GLY* 4.9 4.9 - - - +
147C GLU* 3.0 37.7 + - - +
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.6 27.1 - - + -
99A GLY 4.3 0.7 - - - +
100A ALA* 3.7 25.1 - - - +
103A PRO* 4.9 10.3 - - + -
104A ASN* 3.7 37.1 - - + +
107A PHE* 3.7 40.6 - + + -
131A VAL* 3.1 38.1 + - + -
132A ASN* 1.3 68.7 + - - +
134A ASP* 1.4 63.3 + - - +
136A LEU* 3.8 1.7 + - - +
137A PHE* 3.2 26.9 + - - +
286E MET* 3.5 25.7 - - + +
288E VAL* 4.6 7.9 - - + -
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 3.0 29.4 + - + +
100A ALA* 3.9 15.2 + - + +
132A ASN* 3.2 19.6 + - - +
133A PHE* 1.4 78.8 - - - +
135A ALA* 1.4 55.1 + - - +
137A PHE* 3.4 3.1 + - - +
138A MET* 2.9 51.3 + - - +
144A GLN* 5.6 2.6 - - - +
145C ALA 5.4 4.5 - - - +
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN* 3.2 27.1 + - - +
134A ASP* 1.4 82.6 - - - +
136A LEU* 1.3 58.5 + - + +
138A MET* 2.9 9.9 + - - +
139A ASN* 2.6 41.4 + - - +
144A GLN* 5.8 3.1 - - + +
146C GLY* 4.9 4.9 - - - -
147C GLU* 3.3 24.9 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A VAL* 4.4 21.1 - - + -
132A ASN 3.3 21.6 + - - +
133A PHE* 4.4 1.8 - - - +
135A ALA* 1.3 86.2 - - + +
137A PHE* 1.3 59.6 + - - +
139A ASN* 3.5 24.4 + - - +
140A TYR* 3.8 6.6 + - - +
147C GLU* 4.7 5.4 - - - +
286E MET* 3.7 28.4 - - + +
287E PRO 3.4 13.2 - - - +
288E VAL* 4.6 2.9 - - + -
289E ARG* 3.4 39.0 - - - +
309G THR 5.9 2.9 - - - +
310G PRO* 6.0 2.9 - - + +
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Residues in contact with PHE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR* 4.4 3.6 - - - -
95A ALA* 3.6 33.0 - - + -
96A HIS* 3.6 33.2 - + + -
99A GLY* 4.3 14.1 - - - +
100A ALA* 4.7 0.9 - - + -
133A PHE 3.2 21.4 + - - +
134A ASP* 3.6 4.5 - - - +
136A LEU* 1.3 74.1 - - - +
138A MET* 1.4 61.0 + - + +
140A TYR* 3.4 20.4 + + - +
141A LEU* 2.9 60.9 + - + +
280E LEU* 5.4 2.5 - - + -
285E ASN* 4.3 18.6 - - + -
286E MET* 4.2 17.8 - - + +
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 4.8 7.0 - - + -
96A HIS* 5.4 6.1 - - + +
134A ASP* 2.9 42.3 + - - +
135A ALA* 2.9 11.9 + - - +
137A PHE* 1.4 73.7 - - + +
139A ASN* 1.4 57.7 + - - +
140A TYR 3.0 1.6 - - - -
141A LEU* 3.0 39.8 + - + -
142A GLN* 3.1 19.6 + - + -
143A GLN* 2.8 30.3 + - - +
144A GLN* 3.7 37.7 - - + -
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ALA* 2.6 39.9 + - - +
136A LEU* 3.6 17.3 - - - +
137A PHE 3.3 0.6 - - - -
138A MET* 1.4 75.9 - - - +
140A TYR* 1.3 59.4 + - - +
143A GLN* 4.5 13.5 + - - +
144A GLN 4.7 12.5 + - - +
1C MET* 5.4 7.8 - - - +
289E ARG* 5.8 1.7 + - - -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.1 28.1 - - + +
136A LEU 3.8 6.8 + - - +
137A PHE* 3.4 24.0 + + - +
138A MET 3.0 0.2 - - - -
139A ASN* 1.3 82.0 - - - +
141A LEU* 1.3 75.7 + - + +
142A GLN 3.6 0.6 + - - -
143A GLN 5.0 0.3 + - - -
285E ASN 6.1 1.1 - - - -
286E MET* 6.2 2.2 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 56.9 + - + +
3A GLU* 3.5 29.4 - - + +
92A THR* 3.3 26.7 - - - +
96A HIS* 5.1 6.3 - - + -
137A PHE* 2.9 42.7 + - + +
138A MET* 3.0 24.1 + - + -
140A TYR* 1.3 87.0 - - + +
142A GLN* 1.3 59.1 + - - +
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Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 2.7 25.1 + - - +
3A GLU* 3.6 20.9 - - + +
138A MET* 3.1 18.6 + - + -
140A TYR 3.6 0.6 - - - -
141A LEU* 1.3 76.6 - - - +
143A GLN* 1.4 78.7 + - - +
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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