Contacts of the helix formed by residues 114 - 126 (chain t) 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 t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76t TYR* 2.9 21.2 + - + +
112t ASN 3.7 2.3 + - - +
113t ALA* 1.3 70.9 - - - +
115t PRO* 1.4 62.5 - - - +
116t GLN* 2.8 26.7 + - - +
117t VAL* 2.7 39.0 + - + +
118t LEU* 3.0 9.8 + - - +
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Residues in contact with PRO 115 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104t LYS* 4.5 8.5 - - - +
108t ILE* 3.9 28.7 - - + -
113t ALA 3.3 9.8 - - - +
114t ASN* 1.4 89.7 - - - +
116t GLN* 1.3 56.2 + - - +
118t LEU* 3.3 13.9 + - + +
119t ASP* 2.9 37.9 + - - +
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Residues in contact with GLN 116 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66t TYR* 3.2 36.0 + - + -
114t ASN* 2.8 22.6 + - - +
115t PRO* 1.3 74.5 - - - +
117t VAL* 1.3 61.8 + - + +
119t ASP* 3.4 9.9 + - - +
120t ALA* 3.1 18.2 + - - +
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Residues in contact with VAL 117 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62t VAL* 5.5 0.4 - - + -
63t LEU* 3.6 30.5 - - + -
66t TYR* 3.9 29.8 - - + -
68t ILE* 4.3 14.6 - - + -
76t TYR* 3.7 29.8 - - + +
114t ASN* 2.7 23.0 + - + +
116t GLN* 1.3 73.0 - - + +
118t LEU* 1.3 65.3 + - - +
120t ALA* 3.0 9.8 + - + +
121t VAL* 2.9 22.9 + - + +
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Residues in contact with LEU 118 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76t TYR* 3.7 21.8 - - + -
79t PHE* 3.3 53.7 - - + -
104t LYS* 4.0 18.2 - - + +
107t TYR* 4.4 1.8 - - + -
108t ILE* 3.3 35.4 - - + +
113t ALA* 3.8 19.1 - - + -
114t ASN 3.0 12.1 + - - +
115t PRO* 3.5 15.0 - - + +
117t VAL* 1.3 76.9 - - - +
119t ASP* 1.3 61.1 - - - +
121t VAL* 3.2 3.3 + - - -
122t VAL* 3.1 20.1 + - - +
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Residues in contact with ASP 119 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104t LYS* 2.7 36.5 + - - +
115t PRO* 2.9 21.6 + - - +
116t GLN* 3.6 11.6 - - - +
117t VAL 3.2 0.2 - - - -
118t LEU* 1.3 72.3 - - - +
120t ALA* 1.3 61.3 + - - +
122t VAL* 3.1 8.4 + - - +
123t ASN* 2.8 42.6 + - - +
129t PRO* 5.4 13.2 - - + +
130t THR* 5.2 3.8 - - - +
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Residues in contact with ALA 120 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62t VAL* 3.8 11.6 - - + +
66t TYR* 3.5 40.4 - - + +
116t GLN* 3.1 5.0 + - - +
117t VAL* 3.0 10.6 + - - +
119t ASP* 1.3 78.2 - - - +
121t VAL* 1.3 63.9 + - - +
123t ASN* 3.1 20.7 + - - +
124t ILE* 3.3 17.7 + - - +
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Residues in contact with VAL 121 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59t VAL* 4.1 27.1 - - + -
62t VAL* 5.4 4.7 - - + -
63t LEU* 5.0 2.2 - - + -
76t TYR* 4.2 21.8 - - + +
79t PHE* 3.8 12.3 - - + -
80t GLY* 3.5 32.3 - - - -
117t VAL* 2.9 21.9 + - + +
118t LEU* 3.5 7.9 - - - +
119t ASP 3.2 0.2 - - - -
120t ALA* 1.3 77.6 - - + +
122t VAL* 1.3 62.9 + - - +
124t ILE* 3.0 18.2 + - - +
125t ILE* 3.2 18.9 + - + +
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Residues in contact with VAL 122 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79t PHE* 3.7 23.1 - - + -
83t VAL* 4.6 7.0 - - + -
100t ILE* 4.3 20.9 - - + -
104t LYS* 6.0 1.6 - - + -
118t LEU 3.1 14.4 + - - +
119t ASP* 3.1 12.8 + - - +
121t VAL* 1.3 75.5 - - - +
123t ASN* 1.3 54.3 + - - +
124t ILE 3.0 0.5 + - - -
125t ILE* 4.6 5.2 - - - +
126t THR* 2.5 53.0 + - + +
128t SER 3.2 22.0 - - - +
129t PRO* 4.3 6.5 - - + -
130t THR* 4.4 9.0 - - + +
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Residues in contact with ASN 123 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123O ASN* 3.8 21.5 + - - +
124O ILE* 3.9 0.7 - - - +
127O GLY 5.3 5.2 - - - +
119t ASP* 2.8 28.6 + - - +
120t ALA* 3.1 12.1 + - - +
122t VAL* 1.3 75.0 - - - +
124t ILE* 1.3 59.2 + - + +
127t GLY* 3.2 26.6 - - - +
128t SER* 3.1 1.0 - - - -
129t PRO* 3.0 45.3 - - - +
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Residues in contact with ILE 124 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O ASN* 4.7 6.5 + - - +
124O ILE* 4.1 28.1 - - + +
126O THR 5.0 0.7 - - - +
127O GLY* 3.4 33.7 - - - +
55t VAL* 5.6 1.6 - - - +
58t ASN* 3.6 38.8 - - + +
59t VAL* 4.7 5.8 - - + +
62t VAL* 3.7 24.9 - - + -
120t ALA 3.3 14.8 - - - +
121t VAL* 3.0 8.9 + - - +
122t VAL 3.0 0.8 - - - -
123t ASN* 1.3 83.8 - - + +
125t ILE* 1.3 72.1 + - + +
127t GLY 3.9 3.5 + - - -
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Residues in contact with ILE 125 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O ASN* 4.8 10.6 - - - +
61O ALA* 6.1 0.7 - - - +
55t VAL* 4.0 26.2 - - + -
59t VAL* 4.7 1.6 - - + -
80t GLY* 3.1 42.6 - - - +
83t VAL* 3.8 25.6 - - + -
84t ALA* 4.4 14.6 - - + +
87t LEU* 4.5 19.1 - - + +
121t VAL* 3.2 19.8 + - + +
122t VAL 4.2 1.6 - - - +
124t ILE* 1.3 83.6 - - + +
126t THR* 1.3 62.7 + - + +
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Residues in contact with THR 126 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ALA* 5.7 3.6 - - - +
62O VAL* 5.4 4.2 - - - +
65O GLN* 3.9 22.7 + - - +
124O ILE* 4.8 1.9 - - - +
83t VAL* 4.5 4.0 - - + -
87t LEU* 6.0 2.7 - - + -
96t LEU* 4.8 11.2 - - + -
100t ILE* 4.1 20.4 - - + -
122t VAL* 2.5 35.9 + - + +
124t ILE 4.4 0.4 - - - -
125t ILE* 1.3 84.8 - - + +
127t GLY* 1.3 58.1 + - - +
128t SER* 2.5 30.1 + - - +
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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
------------------------------------------------------------
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