Contacts of the helix formed by residues 117 - 123 (chain A) in PDB entry 1QXP
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 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A SER 4.9 1.6 + - - -
114A LEU 3.0 26.8 + - - +
115A THR 4.7 1.3 - - - -
116A LEU* 1.3 76.6 - - + +
118A GLU* 1.4 63.0 + - - +
119A THR* 2.8 9.5 + - - -
120A ILE* 2.8 51.2 + - + +
121A LEU* 3.1 18.5 + - - +
237A LEU* 5.4 2.4 - - + +
348A LEU* 3.7 23.6 - - - +
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Residues in contact with GLU 118 (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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90A ASP* 5.5 9.4 - - + +
91A GLY 6.3 0.4 - - - +
115A THR 4.6 5.0 - - - +
116A LEU 3.3 17.5 - - - +
117A ASN* 1.4 74.1 + - - +
119A THR* 1.3 66.4 + - - +
121A LEU* 3.7 6.0 + - - +
122A HIS* 3.0 39.9 + - + +
127A TYR* 5.8 0.7 - - - +
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Residues in contact with THR 119 (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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117A ASN* 3.1 10.1 - - - -
118A GLU* 1.3 63.8 - - - +
120A ILE* 1.3 67.0 + - - +
122A HIS* 3.9 2.9 + - - +
123A ARG* 3.3 28.7 + - - +
127A TYR* 5.3 3.6 - - - -
348A LEU* 3.8 29.6 - - + +
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Residues in contact with ILE 120 (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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113A SER 5.9 0.2 - - - +
114A LEU* 3.6 26.2 - - + +
117A ASN* 2.8 43.8 + - + +
119A THR* 1.3 82.4 - - - +
121A LEU* 1.3 62.5 + - - +
123A ARG* 3.4 22.9 + - - +
124A VAL* 4.1 9.7 + - - +
207A PHE 4.4 2.3 - - - +
208A THR* 4.5 16.8 - - + -
237A LEU* 3.2 41.1 - - + -
342A ASN* 3.9 15.9 - - - +
348A LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 121 (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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88A ILE* 4.7 7.9 - - + -
90A ASP* 5.1 10.3 - - - +
114A LEU* 3.2 39.7 - - + +
115A THR* 4.3 13.7 - - + +
117A ASN 3.1 11.6 + - - +
118A GLU* 3.8 7.4 - - - +
120A ILE* 1.3 80.6 - - - +
122A HIS* 1.4 76.2 + - + +
123A ARG 3.2 1.1 - - - -
124A VAL* 3.1 5.2 + - - +
125A VAL* 2.7 36.5 + - + +
177A TRP* 3.6 27.8 - - + -
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Residues in contact with HIS 122 (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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21A HIS* 5.6 0.3 - - - -
88A ILE* 3.6 24.1 - - + +
90A ASP* 5.6 6.3 + - + +
118A GLU* 3.0 32.6 + - + +
119A THR 4.7 1.8 - - - +
121A LEU* 1.4 89.0 - - + +
123A ARG* 1.4 57.3 + - - +
124A VAL 3.0 7.2 - - - -
125A VAL* 2.5 44.4 + - - +
126A PRO* 3.1 12.9 - - - +
127A TYR* 2.9 60.5 + + + +
142A GLN* 5.7 0.2 + - - -
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Residues in contact with ARG 123 (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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21A HIS* 2.5 69.1 + - + +
119A THR* 3.3 28.2 + - - +
120A ILE* 3.4 19.5 + - - +
122A HIS* 1.4 76.5 - - - +
124A VAL* 1.4 58.5 + - + +
126A PRO 5.3 0.2 - - - -
142A GLN* 3.4 12.1 + - - +
149A TRP* 4.2 11.2 - - + +
207A PHE 5.2 1.7 + - - +
208A THR* 3.3 30.7 + - - +
342A ASN* 6.3 0.6 - - - -
343A LEU* 4.3 10.5 - - - +
345A PRO* 2.8 43.5 + - - +
348A LEU* 5.2 4.2 - - - +
349A LYS* 5.3 3.8 - - - +
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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