Contacts of the helix formed by residues 114 - 126 (chain f) 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 f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76f TYR* 2.9 21.1 + - + +
112f ASN 3.7 2.3 + - - +
113f ALA* 1.3 70.8 - - - +
115f PRO* 1.4 62.4 - - - +
116f GLN* 2.8 26.6 + - - +
117f VAL* 2.7 39.5 + - + +
118f LEU* 3.0 10.0 + - - +
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Residues in contact with PRO 115 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104f LYS* 4.5 8.1 - - - +
108f ILE* 3.9 28.5 - - + -
113f ALA 3.3 10.3 - - - +
114f ASN* 1.4 90.3 - - - +
116f GLN* 1.3 56.1 + - - +
118f LEU* 3.3 13.4 + - + +
119f ASP* 2.9 38.1 + - - +
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Residues in contact with GLN 116 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66f TYR* 3.2 36.3 + - + -
114f ASN* 2.8 23.9 + - - +
115f PRO* 1.3 75.1 - - - +
117f VAL* 1.3 62.4 + - + +
119f ASP* 3.4 9.7 + - - +
120f ALA* 3.1 18.4 + - - +
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Residues in contact with VAL 117 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62f VAL* 5.5 0.9 - - + -
63f LEU* 3.6 31.0 - - + -
66f TYR* 3.9 29.8 - - + -
68f ILE* 4.3 15.0 - - + -
76f TYR* 3.7 28.9 - - + +
114f ASN* 2.7 22.2 + - + +
116f GLN* 1.3 71.6 - - + +
118f LEU* 1.3 65.9 + - - +
120f ALA* 3.0 9.5 + - + +
121f VAL* 2.9 22.8 + - + +
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Residues in contact with LEU 118 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76f TYR* 3.7 21.1 - - + -
79f PHE* 3.3 52.6 - - + -
104f LYS* 4.0 18.8 - - + +
107f TYR* 4.4 1.8 - - + -
108f ILE* 3.3 34.8 - - + +
113f ALA* 3.8 20.0 - - + -
114f ASN 3.0 11.5 + - - +
115f PRO* 3.5 14.4 - - + +
117f VAL* 1.3 77.3 - - - +
119f ASP* 1.3 61.3 + - - +
121f VAL* 3.2 3.1 + - - +
122f VAL* 3.1 20.4 + - - +
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Residues in contact with ASP 119 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104f LYS* 2.7 36.2 + - - +
115f PRO* 2.9 21.9 + - - +
116f GLN* 3.6 12.4 - - - +
117f VAL 3.2 0.2 - - - -
118f LEU* 1.3 73.1 - - - +
120f ALA* 1.3 62.1 + - - +
122f VAL* 3.1 8.3 + - - +
123f ASN* 2.8 42.6 + - - +
129f PRO* 5.4 12.9 - - + +
130f THR* 5.2 3.8 + - - +
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Residues in contact with ALA 120 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62f VAL* 3.8 12.3 - - + +
66f TYR* 3.5 39.9 - - + +
116f GLN* 3.1 5.5 + - - +
117f VAL* 3.0 10.4 + - - +
119f ASP* 1.3 79.3 - - - +
121f VAL* 1.3 62.9 + - - +
123f ASN* 3.1 20.6 + - - +
124f ILE* 3.3 17.8 + - - +
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Residues in contact with VAL 121 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59f VAL* 4.1 26.7 - - + -
62f VAL* 5.4 4.0 - - + -
63f LEU* 5.0 2.7 - - + -
76f TYR* 4.2 22.0 - - + +
79f PHE* 3.8 12.8 - - + -
80f GLY* 3.5 32.5 - - - +
117f VAL* 2.9 21.9 + - + +
118f LEU* 3.5 7.4 - - - +
119f ASP 3.2 0.2 - - - -
120f ALA* 1.3 76.0 - - + +
122f VAL* 1.3 63.0 + - - +
124f ILE* 3.0 18.4 + - - +
125f ILE* 3.2 19.1 + - + +
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Residues in contact with VAL 122 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79f PHE* 3.7 23.1 - - + -
83f VAL* 4.6 7.4 - - + -
100f ILE* 4.3 21.3 - - + -
104f LYS* 6.0 1.8 - - + -
118f LEU 3.1 13.8 + - - +
119f ASP* 3.1 12.3 + - - +
121f VAL* 1.3 75.6 - - - +
123f ASN* 1.3 55.5 + - - +
124f ILE 3.0 0.7 + - - -
125f ILE* 4.6 4.7 - - - +
126f THR* 2.5 52.4 + - + +
128f SER 3.2 22.0 - - - +
129f PRO* 4.3 6.7 - - + -
130f THR* 4.4 7.9 - - + +
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Residues in contact with ASN 123 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASN* 3.8 21.4 + - - +
124A ILE* 3.9 0.7 - - - +
127A GLY 5.3 4.9 - - - +
119f ASP* 2.8 29.7 + - - +
120f ALA* 3.1 12.1 + - - +
122f VAL* 1.3 74.6 - - - +
124f ILE* 1.3 59.9 + - + +
127f GLY* 3.2 27.0 - - - +
128f SER* 3.1 1.2 - - - -
129f PRO* 3.0 45.6 - - - +
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Residues in contact with ILE 124 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 4.7 6.3 + - - +
123A ASN 4.4 0.2 - - - +
124A ILE* 4.1 28.6 - - + +
126A THR 5.0 0.4 - - - +
127A GLY* 3.4 34.3 - - - +
55f VAL* 6.1 1.1 - - - -
58f ASN* 3.6 39.0 - - + +
59f VAL* 4.7 6.5 - - + +
62f VAL* 3.7 25.4 - - + -
120f ALA 3.3 14.8 - - - +
121f VAL* 3.0 8.7 + - - +
122f VAL 3.0 0.6 - - - -
123f ASN* 1.3 83.6 - - + +
125f ILE* 1.3 73.3 + - + +
126f THR 4.4 0.2 - - - -
127f GLY 3.9 3.2 + - - -
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Residues in contact with ILE 125 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.8 11.0 - - - +
61A ALA* 6.1 0.7 - - - +
55f VAL* 4.0 25.4 - - + -
59f VAL* 4.7 1.8 - - + -
80f GLY* 3.1 42.4 - - - +
83f VAL* 3.8 25.8 - - + -
84f ALA* 4.4 14.8 - - + +
87f LEU* 4.5 19.1 - - + +
121f VAL* 3.2 20.2 + - + +
122f VAL 4.2 1.3 - - - +
124f ILE* 1.3 84.4 - - + +
126f THR* 1.3 62.0 + - + +
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Residues in contact with THR 126 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 5.7 4.2 - - - +
62A VAL* 5.4 4.5 - - - +
65A GLN* 3.9 22.3 + - - +
124A ILE* 4.8 1.5 - - - +
83f VAL* 4.5 4.0 - - + -
87f LEU* 6.0 2.9 - - + -
96f LEU* 4.8 10.5 - - + -
100f ILE* 4.1 20.2 - - + -
122f VAL* 2.5 36.9 + - + +
124f ILE 4.4 0.4 - - - -
125f ILE* 1.3 84.9 - - + +
127f GLY* 1.3 58.5 + - - +
128f SER* 2.5 30.3 + - - -
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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