Contacts of the helix formed by residues 86 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D ASN* 3.5 18.2 - - - +
83D GLU* 3.1 40.1 + - - +
84D VAL 2.9 3.6 + - - +
85D GLY* 1.3 81.2 - - - +
87D PHE* 1.3 61.1 + - - +
88D ARG* 3.1 41.1 - - + +
89D PHE* 2.8 21.0 + - - +
90D LEU* 3.0 12.7 + - - +
130D LYS* 4.2 4.7 - - - +
306H ASP* 3.7 22.7 - - + +
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Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LYS* 1.3 71.6 - - - +
88D ARG* 1.3 55.9 + - - +
89D PHE 2.9 0.2 - - - -
90D LEU* 4.2 10.8 - - + -
91D ASN* 2.7 45.6 + - - +
130D LYS* 3.4 59.1 - - + +
133D ASP* 4.1 21.3 - - + -
306H ASP* 2.7 17.8 + - - +
307H GLU 3.5 23.1 - - - +
308H ASP* 4.4 0.9 - - - -
309H LEU* 3.4 53.6 - - + -
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLN* 5.5 4.9 - - - +
48D ARG* 6.0 1.6 - - - +
83D GLU* 4.0 11.5 + - - +
86D LYS* 3.2 42.5 - - + +
87D PHE* 1.3 72.6 - - - +
89D PHE* 1.3 58.7 + - + +
91D ASN* 4.5 2.1 - - - +
92D GLU* 3.6 20.8 - - - +
305H SER* 3.8 30.4 + - - -
306H ASP* 2.8 30.1 + - - +
307H GLU* 3.6 25.3 - - + +
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Residues in contact with PHE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 3.3 46.0 - - + -
50D LEU* 4.9 1.3 - - + -
51D ALA* 3.7 19.7 - - + -
54D ILE* 5.0 1.6 - - + -
69D LEU* 4.1 27.4 - - + -
83D GLU 3.6 15.9 - - - +
84D VAL* 3.5 40.8 - - + -
86D LYS* 2.8 8.9 + - + +
88D ARG* 1.3 79.8 - - + +
90D LEU* 1.3 68.8 + - + +
91D ASN 3.2 1.6 - - - -
92D GLU* 3.0 22.0 + - - +
93D LEU* 3.4 31.9 + - + +
121D TRP* 4.4 3.4 - + - -
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D VAL 3.5 21.1 - - - +
85D GLY 4.4 0.7 - - - -
86D LYS 3.0 15.3 + - - +
87D PHE* 4.2 8.7 - - + -
89D PHE* 1.3 82.5 - - + +
91D ASN* 1.3 59.1 + - - +
93D LEU* 2.8 29.1 + - + +
94D ILE* 2.9 17.7 + - + +
118D LEU* 3.8 28.9 - - + -
121D TRP* 4.7 4.9 - - + -
130D LYS* 3.3 44.9 - - + +
131D ILE* 3.7 11.9 - - + +
134D ALA* 4.1 13.5 - - + -
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Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 2.7 33.1 + - - +
88D ARG* 4.9 3.4 - - - +
90D LEU* 1.3 72.0 - - - +
92D GLU* 1.3 66.7 + - + +
94D ILE* 3.2 10.7 + - - +
95D LYS* 3.1 30.8 + - - +
307H GLU* 4.0 12.5 - - - +
308H ASP 2.9 23.4 + - - -
309H LEU* 3.7 13.0 - - - +
310H LEU* 2.9 37.2 + - + +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ARG* 5.3 6.4 + - - -
51D ALA* 3.8 25.8 - - + -
55D GLN* 2.9 39.9 + - - +
88D ARG 3.6 21.8 - - - +
89D PHE 3.0 7.6 + - - +
91D ASN* 1.3 79.7 - - - +
93D LEU* 1.3 62.9 + - - +
95D LYS* 3.4 38.5 + - - +
96D VAL* 3.6 9.2 + - - +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ALA* 5.5 2.7 - - - -
54D ILE* 4.1 38.1 - - + -
66D LEU* 5.2 1.1 - - + -
69D LEU* 5.0 1.6 - - + -
89D PHE* 3.4 36.7 + - + +
90D LEU* 2.8 15.2 + - + +
92D GLU* 1.3 78.9 - - + +
94D ILE* 1.3 64.7 + - + +
96D VAL* 3.2 19.0 + - + +
97D VAL* 3.6 10.4 + - - +
114D VAL* 4.1 18.5 - - + +
117D LEU* 6.1 0.9 - - + -
118D LEU* 3.6 28.0 - - + -
121D TRP* 3.9 15.3 - - + -
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Residues in contact with ILE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 2.9 21.3 + - + +
91D ASN* 3.2 10.5 + - - +
93D LEU* 1.3 74.0 - - + +
95D LYS* 1.3 64.9 + - - +
97D VAL* 3.1 10.6 + - - +
98D SER* 2.8 31.2 + - - -
134D ALA* 5.0 14.8 - - + +
137D MSE 4.8 4.9 - - + -
138D LEU* 4.2 21.5 - - + -
309H LEU* 5.1 3.8 - - + -
310H LEU* 3.4 48.5 - - + +
312H ILE* 3.4 24.7 - - + -
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Residues in contact with LYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 5.3 11.1 - - - +
105C ARG* 6.1 0.8 - - - +
55D GLN* 4.2 4.0 - - - +
91D ASN* 3.1 16.1 + - - +
92D GLU* 3.4 41.1 + - - +
93D LEU 3.2 0.2 - - - -
94D ILE* 1.3 83.2 - - - +
96D VAL* 1.3 60.9 + - - +
97D VAL 3.4 0.3 + - - -
98D SER 3.5 2.3 - - - +
101D TYR* 3.5 34.1 - - + +
102D LEU* 3.2 36.6 + - + -
103D GLY 3.4 3.5 + - - -
310H LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ILE* 4.2 12.6 - - + +
55D GLN* 3.5 38.6 - - + -
92D GLU 3.6 6.9 + - - +
93D LEU* 3.2 11.9 + - + +
94D ILE 3.1 0.4 - - - -
95D LYS* 1.3 79.0 - - - +
97D VAL* 1.3 56.2 - - + +
98D SER 3.6 0.2 - - - -
102D LEU* 4.0 10.3 - - + -
103D GLY* 3.7 10.9 + - - -
106D VAL* 3.9 16.5 - - + +
110D VAL* 4.0 27.1 - - + -
111D LYS* 3.6 17.3 - - + +
114D VAL* 4.2 14.1 - - + -
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU 3.9 1.8 - - - +
94D ILE* 3.3 22.0 - - - +
96D VAL* 1.3 79.3 - - + +
98D SER* 1.3 61.5 + - - +
99D PRO* 3.6 6.8 - - - +
103D GLY* 4.3 3.4 - - - -
111D LYS* 3.9 45.0 - - + +
114D VAL* 4.1 20.9 - - + -
115D ILE* 4.2 7.2 - - + -
138D LEU* 4.1 20.0 - - + -
143D ILE* 3.5 32.9 - - + +
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Residues in contact with SER 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE 2.8 16.5 + - - -
95D LYS 3.5 2.2 + - - +
97D VAL* 1.3 78.3 - - - +
99D PRO* 1.3 65.6 - - - +
100D LYS 3.3 7.8 + - - -
101D TYR* 2.9 18.1 + - - -
103D GLY* 2.9 22.2 + - - -
138D LEU* 5.9 0.4 - - - -
143D ILE* 4.5 3.6 - - - -
312H ILE* 2.9 50.8 - - - +
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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