Contacts of the strand formed by residues 134 - 140 (chain C) in PDB entry 1QNN
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 LEU 134 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C LEU* 4.3 4.5 - - + -
96C ALA* 4.0 20.6 - - + +
97C ILE* 3.8 31.0 - - + +
100C GLN* 2.8 25.0 + - - +
101C PHE* 3.9 26.0 - - + -
126C LEU* 4.2 9.4 - - + -
127C ALA 3.2 12.1 - - - +
128C SER* 4.0 9.2 - - - -
132C GLY 4.1 0.7 - - - +
133C LYS* 1.3 86.7 + - - +
135C SER* 1.3 65.3 + - - +
153C LEU* 3.9 24.9 - - + -
191C TYR* 4.0 11.2 - - + -
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Residues in contact with SER 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 4.9 4.0 - - - -
125C TRP 3.6 0.7 - - - +
126C LEU* 3.6 3.9 - - - +
127C ALA* 2.9 35.1 + - - +
133C LYS 5.2 0.7 + - - -
134C LEU* 1.3 79.1 - - - +
136C ILE* 1.3 65.7 + - - +
137C GLU* 2.7 28.9 + - - +
150C LEU* 4.1 11.1 - - - +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 4.0 30.7 - - + -
107C PHE* 4.3 6.5 - - + -
110C GLU* 4.1 13.7 - - + +
111C PHE* 4.0 39.3 - - + +
114C ALA* 4.1 14.8 - - + -
124C VAL* 3.8 26.0 - - + -
125C TRP 3.4 3.6 - - - +
126C LEU* 4.9 0.9 - - + -
135C SER* 1.3 74.8 - - - +
137C GLU* 1.3 66.6 + - - +
138C LYS* 4.1 4.5 + - + +
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Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C TRP 3.8 0.2 - - - +
124C VAL* 3.4 4.3 - - - +
125C TRP* 2.8 41.3 + - + +
127C ALA* 4.1 9.9 - - + -
135C SER* 2.7 31.5 + - - +
136C ILE* 1.3 77.5 - - - +
138C LYS* 1.3 62.6 + - - +
139C GLU* 3.6 16.6 + - + +
145C PRO* 4.1 24.7 - - + -
148C LYS* 3.1 33.0 + - - +
150C LEU* 3.7 11.6 - - - +
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Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ALA* 3.5 34.6 + - + +
117C THR* 2.7 39.0 + - - -
118C LEU* 4.4 18.4 - - + +
123C TRP 3.8 4.5 - - - -
124C VAL* 4.7 2.5 - - + +
136C ILE* 4.1 4.7 + - + +
137C GLU* 1.3 73.6 + - - +
139C GLU* 1.3 64.7 + - - +
140C PRO* 3.6 10.2 - - + +
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Residues in contact with GLU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.1 3.5 - - - +
122C GLY* 3.1 0.7 - - - -
123C TRP* 2.7 45.8 + - + +
125C TRP* 4.1 14.6 - - + -
137C GLU* 4.1 17.8 - - + +
138C LYS* 1.3 77.7 - - - +
140C PRO* 1.3 73.5 - - - +
141C ASN 4.3 0.9 - - - +
143C GLY* 3.4 36.1 - - - +
144C ASN* 3.7 14.1 + - - +
145C PRO* 3.8 18.1 - - + +
148C LYS* 4.7 8.5 - - - +
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Residues in contact with PRO 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.7 8.5 - - + -
119C PHE 6.0 1.1 - - - +
121C SER 3.8 8.3 - - - +
122C GLY* 4.2 0.4 - - - -
138C LYS* 3.6 9.4 - - + +
139C GLU* 1.3 89.3 - - - +
141C ASN* 1.3 73.5 + - + +
143C GLY* 3.2 13.2 + - - -
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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