Contacts of the helix formed by residues 114 - 126 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S TYR* 2.9 21.7 + - - +
112S ASN 3.7 2.5 + - - +
113S ALA* 1.3 69.6 - - - +
115S PRO* 1.3 63.3 - - - +
116S GLN* 2.8 23.2 + - - +
117S VAL* 2.7 46.1 + - + +
118S LEU* 3.0 10.6 + - - +
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Residues in contact with PRO 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104S LYS* 5.0 2.4 - - - +
108S ILE* 3.9 31.0 - - + -
113S ALA 3.2 9.8 - - - +
114S ASN* 1.3 90.7 - - - +
116S GLN* 1.3 56.4 + - - +
118S LEU* 3.2 14.4 + - + +
119S ASP* 2.9 37.8 + - - +
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Residues in contact with GLN 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S TYR* 2.9 44.9 + - - -
114S ASN* 2.8 19.2 + - - +
115S PRO* 1.3 74.1 - - - +
117S VAL* 1.3 68.6 + - - +
119S ASP* 3.3 10.2 + - - +
120S ALA* 3.1 16.7 + - - +
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Residues in contact with VAL 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62S VAL* 5.3 0.4 - - + -
63S LEU* 4.1 13.0 - - + -
66S TYR* 4.1 27.8 - - + -
68S ILE* 4.9 7.6 - - + -
76S TYR* 3.7 37.9 - - + +
114S ASN* 2.7 29.2 + - + +
116S GLN* 1.3 83.4 - - - +
118S LEU* 1.3 66.0 - - - +
120S ALA* 3.0 16.5 + - + +
121S VAL* 3.0 15.1 + - + +
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Residues in contact with LEU 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S TYR* 3.6 24.5 - - + -
79S PHE* 3.3 51.7 - - + -
104S LYS* 4.4 11.7 - - + +
107S TYR* 4.4 8.1 - - + -
108S ILE* 3.3 35.4 - - + -
113S ALA* 3.8 17.9 - - + -
114S ASN 3.0 11.0 + - - +
115S PRO* 3.4 13.2 - - + +
117S VAL* 1.3 76.9 - - - +
119S ASP* 1.3 61.8 + - - +
121S VAL* 3.1 4.2 + - - +
122S VAL* 3.0 19.7 + - - +
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Residues in contact with ASP 119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104S LYS* 2.7 37.6 + - - +
115S PRO* 2.9 19.5 + - - +
116S GLN* 3.6 11.2 - - - +
117S VAL 3.2 0.2 - - - -
118S LEU* 1.3 73.6 - - - +
120S ALA* 1.3 59.7 + - - +
122S VAL* 3.2 8.4 + - - +
123S ASN* 2.8 30.2 + - - +
129S PRO* 4.3 25.5 - - + +
130S THR* 5.6 0.9 + - - +
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Residues in contact with ALA 120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62S VAL* 4.0 9.9 - - + +
66S TYR* 3.5 40.4 - - + +
116S GLN* 3.1 10.7 + - - +
117S VAL 3.0 12.7 + - - +
119S ASP* 1.3 77.9 - - - +
121S VAL* 1.3 60.2 + - - +
123S ASN* 3.3 19.2 + - - +
124S ILE* 3.4 14.8 - - - +
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Residues in contact with VAL 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59S VAL* 4.0 27.8 - - + -
62S VAL* 5.0 8.5 - - + -
63S LEU* 5.1 0.9 - - + -
76S TYR* 4.4 19.3 - - + +
79S PHE* 3.8 12.8 - - + -
80S GLY* 3.6 31.9 - - - +
117S VAL* 3.0 23.2 + - + +
118S LEU* 3.1 8.7 + - - +
120S ALA* 1.3 76.2 - - - +
122S VAL* 1.3 63.1 + - - +
124S ILE* 3.0 17.1 + - - +
125S ILE* 3.2 20.0 + - + +
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Residues in contact with VAL 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S PHE* 3.6 23.8 - - + -
83S VAL* 4.5 7.2 - - + -
100S ILE* 4.2 20.9 - - + -
104S LYS* 5.0 1.1 - - + -
118S LEU 3.0 15.2 + - - +
119S ASP* 3.6 13.2 - - - +
121S VAL* 1.3 74.5 - - - +
123S ASN* 1.3 55.4 + - - +
124S ILE 2.9 1.0 + - - -
125S ILE* 4.6 4.9 - - - +
126S THR* 2.6 52.7 + - + +
128S SER 3.2 19.5 - - - +
129S PRO* 3.9 10.8 - - + -
130S THR* 4.1 7.6 - - - +
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Residues in contact with ASN 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119S ASP 2.8 18.3 + - - +
120S ALA* 3.4 11.4 - - - +
121S VAL 3.2 0.2 - - - -
122S VAL* 1.3 75.0 - - - +
124S ILE* 1.3 60.7 + - - +
127S GLY* 3.1 32.7 + - - +
128S SER* 3.4 16.4 - - - +
129S PRO* 3.5 10.8 - - + +
123x ASN* 3.8 16.8 + - - +
127x GLY 3.4 23.8 + - - -
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Residues in contact with ILE 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58S ASN* 3.7 35.4 - - + +
59S VAL* 5.0 3.1 - - + +
62S VAL* 3.6 24.2 - - + -
120S ALA 3.4 14.6 - - - +
121S VAL* 3.0 7.1 + - - +
122S VAL 3.0 0.8 - - - -
123S ASN* 1.3 89.5 - - - +
125S ILE* 1.3 71.0 + - + +
126S THR 3.4 0.2 - - - -
127S GLY 3.6 4.7 + - - -
58x ASN* 4.3 10.9 + - - +
123x ASN 3.9 4.3 - - - +
124x ILE* 4.1 23.5 - - - +
126x THR 4.8 0.9 - - - +
127x GLY* 3.3 35.0 - - - +
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Residues in contact with ILE 125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S VAL* 3.9 24.7 - - + -
59S VAL* 4.4 6.1 - - + -
80S GLY* 3.2 42.2 - - - +
83S VAL* 3.7 27.4 - - + -
84S ALA* 4.5 14.6 - - + +
87S LEU* 4.8 16.6 - - + +
121S VAL* 3.2 20.9 + - + +
122S VAL* 4.2 1.6 - - - +
124S ILE* 1.3 81.4 - - + +
126S THR* 1.3 61.4 + - + +
58x ASN* 4.2 17.5 - - - +
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Residues in contact with THR 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S VAL* 4.3 11.9 - - + -
87S LEU* 6.1 3.4 - - + -
96S LEU* 4.6 11.7 - - + -
100S ILE* 4.1 18.8 - - + -
122S VAL* 2.6 29.5 + - + +
124S ILE 4.2 0.2 - - - -
125S ILE* 1.3 79.3 - - + +
127S GLY* 1.3 57.3 + - - +
128S SER* 2.4 33.7 + - - -
130S THR* 6.3 0.2 - - - -
134S SER* 5.1 6.6 - - - +
61x ALA* 5.9 2.6 - - - +
62x VAL* 5.0 7.1 - - - +
65x GLN* 6.0 1.0 - - - +
124x ILE* 5.0 1.5 - - - +
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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