Contacts of the helix formed by residues 137 - 142 (chain H) in PDB entry 2QXU
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 MET 137 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H ASP 5.0 3.8 - - - -
134H MET 5.7 0.4 - - - -
135H ILE 4.1 2.8 - - - +
136H VAL* 1.3 77.4 - - - +
138H ASN* 1.3 64.8 + - - +
139H TYR* 3.5 38.6 - - + +
140H LEU* 3.0 31.1 + - + +
141H SER* 3.7 0.7 + - - -
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Residues in contact with ASN 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H TYR* 3.6 27.8 - - + +
130H SER 2.9 29.4 + - - +
131H SER* 3.4 9.7 - - - +
133H ASP* 4.5 2.6 - - - +
136H VAL 3.9 6.8 - - - +
137H MET* 1.3 72.0 - - - +
139H TYR* 1.3 62.5 + - - +
141H SER* 2.9 18.8 + - - +
142H ARG* 3.1 18.9 + - + +
150H GLN* 3.4 26.7 + - - +
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Residues in contact with TYR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ARG* 2.7 39.3 + - + -
137H MET* 3.2 40.2 + - + -
138H ASN* 1.3 78.7 - - - +
140H LEU* 1.3 82.7 + - + +
141H SER 3.5 0.2 + - - -
142H ARG* 3.7 17.2 + - - +
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H GLY 3.6 1.6 - - - -
105H ALA* 4.4 10.1 - - + -
106H ASN* 3.1 5.9 + - - +
107H ARG* 2.9 46.5 + - + +
108H LEU* 4.5 23.6 - - + -
136H VAL* 4.2 13.9 - - + -
137H MET* 3.0 30.6 + - + +
139H TYR* 1.3 120.6 - - + +
141H SER* 1.3 57.6 + - - +
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Residues in contact with SER 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLY* 3.5 8.3 - - - -
104H GLY 2.6 34.0 + - - -
106H ASN* 3.0 11.9 + - - +
127H SER* 2.6 25.8 + - - -
128H ILE 5.0 0.2 - - - -
129H TYR* 3.8 26.4 - - - +
136H VAL* 3.9 8.5 + - - +
137H MET 4.1 2.4 + - - -
138H ASN* 2.9 10.1 + - - -
140H LEU* 1.3 79.7 - - - +
142H ARG* 1.3 62.3 + - - +
143H LEU* 3.4 1.6 + - - +
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Residues in contact with ARG 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H ARG* 2.7 37.6 + - - +
129H TYR* 3.4 38.6 + - + +
138H ASN* 3.1 16.0 + - - +
139H TYR* 3.8 11.8 - - - +
140H LEU 3.6 0.4 - - - -
141H SER* 1.3 77.5 - - - +
143H LEU* 1.3 54.3 + - - +
148H ASN* 3.5 24.6 - - - +
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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