Contacts of the helix formed by residues 86 - 98 (chain C) in PDB entry 1JPL
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 LYS 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C ASN* 3.3 24.8 + - - +
83C GLU* 3.6 30.7 - - - +
84C VAL 2.9 2.6 + - - +
85C GLY* 1.3 81.3 - - - +
87C PHE* 1.3 64.4 + - - +
88C ARG* 3.6 35.0 - - + +
89C PHE* 3.2 3.8 + - - -
90C LEU* 3.0 24.8 + - - +
130C LYS* 4.0 6.7 - - - +
306G ASP* 3.5 22.4 - - + +
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Residues in contact with PHE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C LYS* 1.3 70.1 - - - +
88C ARG* 1.3 59.7 + - - +
90C LEU* 3.8 9.6 - - + -
91C ASN* 2.7 50.3 + - - +
130C LYS* 3.6 49.5 - - + +
133C ASP* 4.0 18.2 - - + -
306G ASP* 2.8 18.2 + - - -
307G GLU 3.4 27.1 - - - +
308G ASP* 4.0 1.6 - - - +
309G LEU* 3.4 50.3 - - + -
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLN* 6.3 0.2 - - - +
48C ARG* 5.7 9.2 - - + +
83C GLU* 4.6 7.7 + - - -
86C LYS* 3.1 33.3 - - + +
87C PHE* 1.3 77.0 - - - +
89C PHE* 1.3 59.3 + - - +
91C ASN* 4.6 2.6 - - - +
92C GLU* 3.5 19.6 + - - +
105D ARG* 5.4 11.2 + - - +
305G SER* 2.9 38.5 + - - -
306G ASP* 3.1 15.8 + - - +
307G GLU* 3.8 27.2 + - - +
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Residues in contact with PHE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.3 44.6 - - + -
50C LEU* 4.9 1.8 - - + -
51C ALA* 4.0 18.4 - - + -
54C ILE* 4.9 0.7 - - + -
69C LEU* 3.9 31.2 - - + -
83C GLU 3.7 18.2 - - - +
84C VAL* 3.4 45.5 - - + -
86C LYS* 3.2 3.5 + - - +
87C PHE 3.1 0.2 - - - -
88C ARG* 1.3 77.8 - - + +
90C LEU* 1.3 61.0 + - + +
91C ASN 3.1 1.6 - - - -
92C GLU* 2.9 30.1 + - - +
93C LEU* 3.5 31.7 + - + +
121C TRP* 4.5 1.6 - + - -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 2.9 35.2 - - + +
85C GLY 4.1 0.9 - - - -
86C LYS 3.0 14.7 + - - +
87C PHE* 4.0 8.5 - - + -
89C PHE* 1.3 89.2 - - + +
91C ASN* 1.3 59.3 + - - +
93C LEU* 3.2 10.4 + - + +
94C ILE* 3.1 27.2 + - - +
118C LEU* 4.3 19.6 - - + +
130C LYS* 3.5 41.5 - - + +
131C ILE* 3.7 17.5 - - + +
134C ALA* 4.2 16.6 - - + -
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Residues in contact with ASN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PHE* 2.7 33.9 + - - +
88C ARG* 4.6 3.3 - - - +
90C LEU* 1.3 68.6 - - - +
92C GLU* 1.3 68.3 + - + +
93C LEU 3.0 1.8 - - - -
94C ILE* 3.1 24.1 - - - +
95C LYS* 3.1 14.8 + - + +
307G GLU* 4.1 10.9 - - - +
308G ASP 2.9 24.4 + - - -
309G LEU* 3.6 13.7 - - - +
310G LEU* 2.7 39.8 + - + +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 3.9 26.5 - - + +
55C GLN* 2.9 33.3 + - + +
88C ARG 3.5 20.5 - - - +
89C PHE* 2.9 10.1 + - - +
91C ASN* 1.3 79.9 - - - +
93C LEU* 1.3 63.2 + - + +
95C LYS* 2.8 34.3 + - - +
96C VAL* 3.4 15.8 + - - +
105D ARG* 3.4 29.1 + - - -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 5.8 1.8 - - - -
54C ILE* 4.2 36.3 - - + -
66C LEU* 5.1 1.1 - - + -
69C LEU* 4.9 3.6 - - + -
89C PHE* 3.7 36.6 - - + +
90C LEU* 3.2 13.2 + - + +
91C ASN 3.0 0.2 - - - -
92C GLU* 1.3 77.5 - - + +
94C ILE* 1.3 62.8 + - + +
95C LYS 3.1 1.8 - - - -
96C VAL* 3.0 25.7 - - + +
97C VAL* 3.6 7.7 + - - +
114C VAL* 4.1 23.7 - - + +
117C LEU* 6.5 0.2 - - + -
118C LEU* 4.0 29.4 - - + -
121C TRP* 4.1 10.5 - - + -
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU 3.1 17.7 + - - +
91C ASN* 3.1 20.9 - - - +
93C LEU* 1.3 76.8 - - + +
95C LYS* 1.3 59.6 + - - +
97C VAL* 3.2 11.8 + - - +
98C SER* 3.0 31.5 + - - -
118C LEU* 5.7 2.5 - - + -
134C ALA* 4.7 17.7 - - + +
137C MSE 5.9 2.5 - - + -
138C LEU* 4.4 21.7 - - + +
309G LEU* 5.1 5.6 - - + -
310G LEU* 3.1 39.7 - - + +
312G ILE* 3.2 33.9 - - + -
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLN* 4.2 11.2 + - - +
91C ASN* 3.1 13.9 + - + +
92C GLU* 2.8 38.9 + - - +
93C LEU 3.1 0.4 - - - -
94C ILE* 1.3 85.7 - - - +
96C VAL* 1.3 59.8 + - - +
97C VAL 3.5 0.2 + - - -
98C SER 3.6 2.9 - - - +
101C TYR* 3.2 38.5 - - + +
102C LEU* 2.9 37.3 + - + +
102D LEU* 5.6 8.5 - - - +
105D ARG* 5.9 0.6 - - - +
310G LEU* 3.5 18.6 - - + -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 4.3 13.0 - - + +
55C GLN* 3.6 29.8 - - + -
92C GLU 3.4 16.4 - - - +
93C LEU* 3.0 21.3 - - - +
95C LYS* 1.3 78.1 - - - +
97C VAL* 1.3 60.8 - - + +
98C SER 3.5 0.2 - - - -
102C LEU* 4.1 13.0 - - + -
103C GLY* 3.5 5.3 - - - -
106C VAL* 3.0 38.9 - - + +
110C VAL* 5.4 4.7 - - + -
111C LYS* 3.5 1.4 - - + +
114C VAL* 3.7 28.7 - - + -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LEU 3.6 8.1 - - - +
94C ILE* 3.3 19.3 - - - +
96C VAL* 1.3 92.3 - - + +
98C SER* 1.3 59.4 + - - +
99C PRO* 3.8 5.9 - - - +
103C GLY* 4.4 0.4 - - - -
111C LYS* 3.7 35.6 - - + +
114C VAL* 3.8 24.0 - - + -
115C ILE* 4.2 8.5 - - + -
138C LEU* 4.1 25.1 - - + -
143C ILE* 3.5 25.3 - - + +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE 3.0 16.3 + - - -
95C LYS 3.7 0.6 + - - -
96C VAL 3.5 0.4 - - - -
97C VAL* 1.3 79.8 - - - +
99C PRO* 1.3 63.4 - - - +
100C LYS* 3.4 11.8 + - - +
101C TYR* 2.9 18.7 + - - -
102C LEU 3.4 1.9 + - - -
103C GLY* 2.8 21.4 + - - -
138C LEU* 5.7 0.4 - - - -
143C ILE* 4.7 3.1 - - - -
312G ILE* 3.0 47.3 - - - +
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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