Contacts of the helix formed by residues 114 - 126 (chain h) in PDB entry 3J9X
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 114 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76h TYR* 2.9 21.7 + - + +
112h ASN 3.7 2.3 + - - +
113h ALA* 1.3 70.0 - - - +
115h PRO* 1.4 62.0 - - - +
116h GLN* 2.8 26.7 + - - +
117h VAL* 2.7 38.9 + - + +
118h LEU* 3.0 11.0 + - - +
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Residues in contact with PRO 115 (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 LYS* 4.5 8.3 - - - +
108h ILE* 3.9 29.2 - - + -
113h ALA 3.3 10.1 - - - +
114h ASN* 1.4 89.8 - - - +
116h GLN* 1.3 55.6 + - - +
118h LEU* 3.5 13.9 - - + +
119h ASP* 2.9 38.3 + - - +
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Residues in contact with GLN 116 (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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66h TYR* 3.2 36.5 + - + -
114h ASN* 2.8 24.1 + - - +
115h PRO* 1.3 75.5 - - - +
117h VAL* 1.3 62.5 + - + +
119h ASP* 3.4 10.5 + - - +
120h ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 117 (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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62h VAL* 5.5 0.7 - - + -
63h LEU* 3.6 31.2 - - + -
66h TYR* 3.9 29.8 - - + -
68h ILE* 4.3 15.3 - - + -
76h TYR* 3.7 29.4 - - + +
114h ASN* 2.7 22.0 + - + +
116h GLN* 1.3 72.6 - - + +
118h LEU* 1.3 66.7 + - - +
120h ALA* 3.0 9.6 + - + +
121h VAL* 2.9 22.1 + - + +
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Residues in contact with LEU 118 (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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76h TYR* 3.7 21.5 - - + -
79h PHE* 3.3 54.4 - - + -
104h LYS* 4.0 18.2 - - + +
107h TYR* 4.4 1.6 - - + -
108h ILE* 3.3 35.2 - - + +
113h ALA* 3.8 19.1 - - + -
114h ASN 3.0 11.7 + - - +
115h PRO* 3.5 13.7 - - + +
117h VAL* 1.3 76.5 - - - +
119h ASP* 1.3 63.5 + - - +
121h VAL* 3.2 2.7 + - - -
122h VAL* 3.1 20.0 + - - +
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Residues in contact with ASP 119 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104h LYS* 2.7 36.7 + - - +
115h PRO* 2.9 21.7 + - - +
116h GLN* 3.6 11.7 - - - +
118h LEU* 1.3 72.9 - - - +
120h ALA* 1.3 60.6 + - - +
122h VAL* 3.1 9.5 + - - +
123h ASN* 2.8 43.0 + - - +
129h PRO* 5.4 14.3 - - + +
130h THR* 5.2 3.6 - - - +
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Residues in contact with ALA 120 (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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62h VAL* 3.8 11.4 - - + +
66h TYR* 3.5 41.1 - - + +
116h GLN* 3.1 4.8 + - - +
117h VAL* 3.0 10.7 + - - +
119h ASP* 1.3 78.7 - - - +
121h VAL* 1.3 62.4 + - - +
123h ASN* 3.1 20.4 + - - +
124h ILE* 3.3 18.0 + - - +
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Residues in contact with VAL 121 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59h VAL* 4.1 26.0 - - + +
62h VAL* 5.4 4.0 - - + -
63h LEU* 5.0 2.5 - - + -
76h TYR* 4.2 21.1 - - + +
79h PHE* 3.8 12.1 - - + -
80h GLY* 3.5 32.5 - - - -
117h VAL* 2.9 23.6 + - + +
118h LEU* 3.5 8.3 - - - +
119h ASP 3.2 0.2 - - - -
120h ALA* 1.3 75.3 - - + +
122h VAL* 1.3 63.5 + - + +
124h ILE* 3.0 18.8 + - - +
125h ILE* 3.2 18.6 + - + +
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Residues in contact with VAL 122 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79h PHE* 3.7 24.0 - - + -
83h VAL* 4.6 7.4 - - + -
100h ILE* 4.3 20.9 - - + -
104h LYS* 6.0 1.8 - - + -
118h LEU 3.1 13.6 + - - +
119h ASP* 3.5 11.7 - - - +
121h VAL* 1.3 76.3 - - - +
123h ASN* 1.3 54.8 + - - +
124h ILE 3.0 0.5 + - - -
125h ILE* 4.6 4.5 - - - +
126h THR* 2.5 52.6 + - + +
128h SER 3.2 22.4 - - - +
129h PRO* 4.3 6.7 - - + -
130h THR* 4.4 8.5 - - + +
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Residues in contact with ASN 123 (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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123C ASN* 3.8 20.8 + - - +
124C ILE* 3.9 0.5 - - - +
127C GLY 5.1 5.3 - - - +
119h ASP* 2.8 28.8 + - - +
120h ALA* 3.1 12.5 + - - +
122h VAL* 1.3 74.3 - - - +
124h ILE* 1.3 60.3 + - + +
127h GLY* 3.2 26.7 - - - +
128h SER* 3.1 2.0 - - - -
129h PRO* 3.0 44.4 - - - +
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Residues in contact with ILE 124 (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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58C ASN* 4.7 6.8 + - - +
124C ILE* 4.1 28.0 - - - +
126C THR 5.0 0.7 - - - +
127C GLY* 3.4 33.9 - - - +
55h VAL* 6.1 1.3 - - - -
58h ASN* 3.6 38.4 - - + +
59h VAL* 4.7 7.0 - - + +
62h VAL* 3.7 25.8 - - + -
120h ALA 3.3 15.5 - - - +
121h VAL* 3.4 7.6 - - - +
122h VAL 3.0 0.6 - - - -
123h ASN* 1.3 84.7 - - + +
125h ILE* 1.3 72.3 + - + +
126h THR 3.4 0.6 + - - -
127h GLY 3.9 3.3 + - - -
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Residues in contact with ILE 125 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 4.8 10.4 - - - +
55h VAL* 4.0 25.6 - - + -
59h VAL* 4.6 2.2 - - + -
80h GLY* 3.1 42.4 - - - +
83h VAL* 3.9 27.1 - - + -
84h ALA* 4.4 15.3 - - + +
87h LEU* 4.5 19.8 - - + +
121h VAL* 3.2 19.2 + - + +
122h VAL 4.2 1.1 - - - +
124h ILE* 1.3 84.2 - - + +
126h THR* 1.3 62.7 + - + +
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Residues in contact with THR 126 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 5.7 3.8 - - - +
62C VAL* 5.4 4.5 - - - +
65C GLN* 3.9 22.6 + - - +
124C ILE* 4.8 1.5 - - - +
83h VAL* 4.5 3.8 - - + -
87h LEU* 6.0 2.9 - - + -
96h LEU* 4.8 11.0 - - + -
100h ILE* 4.1 20.6 - - + -
122h VAL* 2.5 36.5 + - + +
124h ILE 4.4 0.4 - - - -
125h ILE* 1.3 85.1 - - + +
127h GLY* 1.3 58.6 + - - +
128h SER* 2.5 30.4 + - - -
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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