Contacts of the helix formed by residues 131 - 137 (chain L) in PDB entry 6QX2
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 ILE 131 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101L TYR* 4.0 24.7 - - + +
102L PRO 3.6 24.2 - - - +
103L LEU* 4.1 13.5 - - + -
129L THR* 3.1 3.6 - - - +
130L LYS* 1.3 75.7 - - - +
132L THR* 1.3 63.5 + - - +
134L GLU* 3.0 22.3 + - + +
135L LEU 3.5 3.8 + - - -
164L PHE* 3.5 32.7 - - + -
188L LEU* 4.1 10.3 - - + -
480L PHE* 3.7 50.3 - - + -
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Residues in contact with THR 132 (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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50L LEU* 4.0 23.6 - - + -
103L LEU* 2.6 49.2 + - - +
128L MET* 3.8 20.9 - - + -
129L THR* 3.0 12.9 + - - -
131L ILE* 1.3 74.7 - - - +
133L LEU* 1.3 64.7 + - - +
135L LEU* 3.1 18.2 + - + +
136L LEU* 3.2 24.5 + - + +
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Residues in contact with LEU 133 (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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54L ASN* 5.5 2.0 - - - +
59L THR* 4.3 10.3 - - + -
60L PRO* 4.0 28.5 - - + -
128L MET* 3.6 26.2 - - + -
129L THR 3.7 2.8 + - - +
130L LYS* 3.2 20.4 - - + +
132L THR* 1.3 77.9 - - - +
134L GLU* 1.3 57.7 - - - +
136L LEU* 3.2 5.4 + - + +
137L ARG* 2.7 36.6 + - - +
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Residues in contact with GLU 134 (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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130L LYS 4.8 0.3 - - - +
131L ILE* 3.0 13.4 + - + +
133L LEU* 1.3 82.2 - - - +
135L LEU* 1.3 64.4 + - - +
136L LEU 3.4 0.3 + - - -
137L ARG* 3.7 10.8 + - - +
163L ARG* 3.0 41.9 + - + +
164L PHE* 4.0 14.6 - - + -
476L ILE* 3.6 26.2 - - + +
479L ARG* 3.3 29.1 + - - -
480L PHE* 3.7 26.0 - - + -
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Residues in contact with LEU 135 (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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40L ASP* 4.5 5.8 - - + +
42L LEU* 4.5 6.3 - - + -
50L LEU* 3.6 27.1 - - + -
103L LEU* 3.8 26.7 - - + -
131L ILE 3.5 2.7 + - - +
132L THR* 3.1 14.6 + - + +
134L GLU* 1.3 76.0 - - - +
136L LEU* 1.3 59.3 + - + +
137L ARG 3.5 0.2 - - - -
160L LEU* 3.5 14.9 - - + +
161L PRO* 3.4 11.1 - - - +
162L ALA* 3.0 44.8 + - + +
164L PHE* 3.6 23.1 - - + +
166L ASN* 3.9 23.1 - - + +
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Residues in contact with LEU 136 (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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50L LEU* 3.7 20.9 - - + +
51L TYR* 4.4 2.7 - - - -
54L ASN* 3.7 38.4 - - + +
128L MET* 3.7 21.1 - - - -
132L THR* 3.2 23.5 + - + +
133L LEU* 3.2 4.9 + - + +
135L LEU* 1.3 77.9 - - + +
137L ARG* 1.3 65.9 + - - +
138L ASP 3.2 0.7 + - - -
139L ILE* 3.0 37.3 + - + +
160L LEU* 3.9 32.3 - - + -
161L PRO* 4.2 3.8 - - - -
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Residues in contact with ARG 137 (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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133L LEU 2.7 16.5 + - - +
134L GLU* 3.7 13.0 + - - +
135L LEU 3.5 2.0 - - - -
136L LEU* 1.3 73.8 - - - +
138L ASP* 1.3 74.4 + - - +
161L PRO* 3.2 22.7 - - - +
163L ARG* 3.9 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