Contacts of the helix formed by residues 112 - 121 (chain A) in PDB entry 1N0U
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 SER 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A HIS* 3.6 24.4 + - - -
109A VAL* 4.8 1.2 - - - +
110A ASP 3.8 2.3 - - - +
111A PHE* 1.3 76.7 - - - +
113A SER* 1.3 62.3 + - - +
114A GLU* 3.4 7.4 + - - -
115A VAL* 3.2 28.4 + - - +
116A THR* 3.4 5.0 + - - -
145A GLN* 2.9 21.6 + - - +
785A ARG* 6.0 0.7 - - - +
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Residues in contact with SER 113 (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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111A PHE 3.9 1.2 + - - -
112A SER* 1.3 71.7 - - - +
114A GLU* 1.3 79.9 + - - +
116A THR* 3.2 12.0 + - - -
117A ALA* 3.1 19.8 + - - +
481A MET* 3.7 30.5 - - - +
482A LYS 6.1 1.3 - - - -
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Residues in contact with GLU 114 (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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106A PRO* 5.0 8.0 - - + +
108A HIS* 4.1 26.0 - - + +
112A SER* 3.2 6.5 - - - +
113A SER* 1.3 86.8 + - - +
115A VAL* 1.3 55.9 + - - +
117A ALA* 2.7 35.5 + - - +
118A ALA* 3.2 6.9 + - - +
465A LYS* 5.3 15.3 + - - +
536A LEU* 4.8 13.3 - - - +
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Residues in contact with VAL 115 (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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105A SER* 6.1 3.4 - - - -
106A PRO* 4.2 13.2 - - + +
107A GLY* 4.2 9.2 - - - +
108A HIS* 3.8 17.5 - - + +
109A VAL* 3.4 30.3 - - + -
112A SER* 3.2 23.5 + - - +
114A GLU* 1.3 76.3 - - - +
116A THR* 1.3 63.3 + - - +
117A ALA 3.1 0.5 + - - -
118A ALA* 3.2 4.3 + - - +
119A LEU* 3.0 41.5 + - + +
142A VAL* 4.1 13.0 - - + -
145A GLN* 4.2 7.2 - - - +
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Residues in contact with THR 116 (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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112A SER 3.4 3.6 + - - -
113A SER* 3.2 13.7 + - - -
114A GLU 3.1 0.6 - - - -
115A VAL* 1.3 77.9 - - - +
117A ALA* 1.3 56.9 + - - +
119A LEU* 3.8 10.4 - - + +
120A ARG* 3.0 39.3 + - - +
145A GLN* 2.8 32.3 + - + +
149A GLU* 3.5 26.9 - - + +
481A MET* 4.0 11.2 - - + -
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Residues in contact with ALA 117 (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 3.1 9.7 + - - +
114A GLU* 2.7 19.8 + - - +
116A THR* 1.3 76.9 - - - +
118A ALA* 1.3 61.9 + - - +
120A ARG* 3.4 17.2 + - - +
121A VAL* 3.8 3.1 + - - +
381A TYR* 4.4 7.1 - - - +
383A SER* 3.0 35.9 + - - +
384A LYS* 5.8 1.6 - - + -
466A THR* 4.4 15.5 - - + -
481A MET* 5.3 3.6 - - + -
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Residues in contact with ALA 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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103A ILE* 4.4 6.3 - - + +
104A ASP 4.0 20.4 - - - +
105A SER* 4.7 6.3 - - - -
106A PRO* 4.4 15.3 - - + -
114A GLU 3.2 5.0 + - - +
115A VAL 3.2 7.5 + - - +
117A ALA* 1.3 77.3 - - - +
119A LEU* 1.3 67.8 + - + +
121A VAL* 3.1 22.7 - - - +
122A THR* 3.6 10.0 - - - +
383A SER* 4.1 6.3 - - - -
384A LYS* 5.9 8.3 - - + +
397A PHE* 6.3 0.2 - - - -
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Residues in contact with LEU 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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23A SER* 4.1 19.5 - - - +
25A ILE* 4.4 11.2 - - + -
105A SER* 6.0 4.0 - - - -
115A VAL* 3.0 41.3 + - + +
116A THR* 3.9 7.2 - - - +
118A ALA* 1.3 78.1 - - + +
120A ARG* 1.3 59.0 + - - +
122A THR* 2.6 35.8 + - - +
125A ALA* 5.6 0.9 - - + -
142A VAL* 4.1 7.6 - - + +
145A GLN* 3.8 13.0 - - + -
146A ALA* 3.7 32.1 - - + +
149A GLU* 4.3 5.8 - - + -
151A ILE* 3.3 24.9 - - + +
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Residues in contact with ARG 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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116A THR* 3.0 21.3 + - - +
117A ALA 3.4 9.0 - - - +
118A ALA 3.2 0.6 - - - -
119A LEU* 1.3 77.3 - - - +
121A VAL* 1.3 54.6 + - - +
122A THR 3.2 0.2 - - - -
149A GLU* 2.8 45.0 + - - +
352A ARG* 2.7 27.1 + - - +
356A LEU* 3.8 20.3 - - + +
381A TYR* 3.4 34.4 + - + +
401A PHE* 3.9 5.5 - - + -
479A LYS* 3.3 56.8 + - - +
481A MET* 2.7 37.7 - - - +
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Residues in contact with VAL 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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21A ASN* 3.8 4.5 - - - +
103A ILE* 3.4 34.6 - - + +
117A ALA 3.8 0.4 + - - -
118A ALA* 3.1 20.2 - - - +
120A ARG* 1.3 75.9 - - - +
122A THR* 1.3 57.6 + - - +
381A TYR* 3.9 16.6 - - + -
383A SER* 3.7 31.0 - - - +
397A PHE* 4.4 7.0 - - + -
398A GLY 4.5 2.0 - - - -
399A ARG* 3.0 53.4 + - + +
401A PHE* 5.2 0.4 - - + -
453A ILE* 4.2 2.5 - - + +
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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