Contacts of the helix formed by residues 86 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ASN* 3.1 25.7 + - - +
83A GLU* 3.2 31.2 + - - +
84A VAL 3.1 2.1 - - - +
85A GLY* 1.3 80.6 - - - +
87A PHE* 1.3 60.7 + - - +
88A ARG* 3.1 38.4 - - + +
89A PHE* 2.9 18.5 + - - +
90A LEU* 3.0 15.6 + - - +
130A LYS* 4.6 4.9 - - - +
305E SER* 4.1 16.8 - - - +
306E ASP* 3.5 17.7 - - - +
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 1.3 68.3 - - - +
88A ARG* 1.3 61.9 + - - +
90A LEU* 4.0 14.1 - - + -
91A ASN* 2.8 48.5 + - - +
130A LYS* 3.5 51.1 - - + -
133A ASP* 4.1 18.8 - - + -
134A ALA 4.6 0.4 - - - -
306E ASP* 3.1 11.3 + - - -
307E GLU 3.4 26.7 - - - +
308E ASP* 4.1 2.0 - - - +
309E LEU* 3.8 44.4 - - + -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 4.9 8.2 - - - +
47A VAL* 6.1 3.6 - - - +
48A ARG* 5.9 11.6 - - + +
83A GLU* 2.8 29.5 + - - -
86A LYS* 3.1 28.5 - - + +
87A PHE* 1.3 78.7 - - - +
89A PHE* 1.3 57.4 + - - +
92A GLU* 3.6 19.9 - - - +
305E SER* 3.8 24.3 + - - -
306E ASP* 2.9 20.7 + - - +
307E GLU* 3.5 26.6 - - + +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.5 42.6 - - + -
48A ARG* 5.6 0.2 - - - -
50A LEU* 4.9 1.8 - - + -
51A ALA* 3.7 23.1 - - + -
54A ILE* 4.9 0.9 - - + -
69A LEU* 3.9 27.4 - - + -
83A GLU 3.7 15.3 - - - +
84A VAL* 3.6 42.8 - - + -
86A LYS* 2.9 7.7 + - - +
88A ARG* 1.3 79.0 - - - +
90A LEU* 1.3 62.0 + - + +
91A ASN 3.2 1.8 - - - -
92A GLU* 2.9 28.7 + - - +
93A LEU* 3.5 33.1 + - + +
121A TRP* 4.5 2.7 - + - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 3.2 27.6 - - + +
85A GLY 4.0 2.0 - - - -
86A LYS 3.0 17.9 + - - +
87A PHE* 4.0 12.6 - - + -
89A PHE* 1.3 84.7 - - + +
91A ASN* 1.3 61.0 + - - +
93A LEU* 3.1 10.8 + - + +
94A ILE* 3.0 27.9 + - + +
118A LEU* 4.0 27.1 - - + +
130A LYS* 3.5 36.8 - - + +
131A ILE* 3.9 12.6 - - + +
134A ALA* 4.2 13.5 - - + -
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Residues in contact with ASN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PHE* 2.8 29.9 + - - +
88A ARG 4.9 0.2 - - - +
90A LEU* 1.3 72.8 - - - +
92A GLU* 1.3 62.4 + - - +
94A ILE* 3.4 6.4 + - - -
95A LYS* 3.2 35.7 + - - +
307E GLU* 2.6 31.4 + - - +
308E ASP 2.8 23.6 + - - -
309E LEU* 3.4 13.3 - - - +
310E LEU* 2.5 42.5 + - + +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 3.8 26.2 - - + -
55A GLN* 2.6 47.8 + - - +
88A ARG 3.6 20.6 - - - +
89A PHE* 2.9 11.8 + - + +
91A ASN* 1.3 77.2 - - - +
93A LEU* 1.3 63.3 + - - +
95A LYS* 3.4 29.7 + - - +
96A VAL* 3.5 9.0 - - - +
307E GLU* 4.6 7.3 - - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 5.6 1.8 - - - -
54A ILE* 4.1 31.6 - - + -
66A LEU* 5.0 0.9 - - + -
69A LEU* 4.8 2.7 - - + -
89A PHE* 3.5 44.1 + - + +
90A LEU* 3.1 11.5 + - + +
92A GLU* 1.3 76.6 - - - +
94A ILE* 1.3 67.0 + - + +
95A LYS 3.2 0.2 - - - -
96A VAL* 3.0 21.6 + - - +
97A VAL* 3.4 10.6 + - - +
114A VAL* 4.2 22.6 - - + +
117A LEU* 6.2 1.1 - - + -
118A LEU* 4.1 22.7 - - + -
121A TRP* 4.0 21.1 - - + -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 3.0 17.7 + - - +
91A ASN* 3.5 17.0 - - - +
92A GLU 3.3 0.2 - - - -
93A LEU* 1.3 78.7 - - + +
95A LYS* 1.3 56.3 + - - +
97A VAL* 3.3 8.4 + - - +
98A SER* 2.8 28.2 + - - -
118A LEU* 5.6 2.9 - - + -
134A ALA* 4.2 16.6 - - + +
137A MSE 4.4 7.4 - - + -
138A LEU* 4.2 27.8 - - + -
309E LEU* 3.7 29.8 - - + -
310E LEU* 4.0 7.2 - - + +
312E ILE* 3.6 29.4 - - + -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN* 3.8 8.5 - - - +
91A ASN* 3.2 19.4 + - - +
92A GLU* 3.4 42.4 + - - +
93A LEU 3.2 0.4 - - - -
94A ILE* 1.3 76.7 - - - +
96A VAL* 1.3 62.2 + - - +
97A VAL 3.4 0.2 + - - -
98A SER 3.5 4.0 - - - +
101A TYR* 3.8 33.2 - - + -
102A LEU* 3.0 33.6 + - + -
103A GLY 3.3 3.6 + - - -
307E GLU* 5.1 2.0 + - - -
310E LEU* 3.6 27.1 - - + +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.3 16.4 - - + +
55A GLN* 3.7 26.0 - - + -
92A GLU 3.5 17.5 - - - +
93A LEU* 3.0 13.4 + - + +
95A LYS* 1.3 78.1 - - - +
97A VAL* 1.3 58.6 + - + +
102A LEU* 4.3 8.5 - - + -
103A GLY* 3.4 17.2 + - - -
106A VAL* 3.7 29.2 - - + +
110A VAL* 3.9 15.7 - - + -
111A LYS* 3.5 11.6 - - + +
114A VAL* 4.4 11.2 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU 3.4 6.3 + - - +
94A ILE* 3.4 11.7 - - - +
96A VAL* 1.3 81.3 - - + +
98A SER* 1.3 64.2 + - - +
99A PRO* 3.4 9.9 - - - +
103A GLY* 4.2 2.0 - - - -
111A LYS* 3.9 45.4 + - + +
114A VAL* 4.0 22.0 - - + -
115A ILE* 4.0 8.3 - - + -
138A LEU* 4.0 23.8 - - + -
143A ILE* 4.0 28.3 - - + +
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Residues in contact with SER 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 2.8 22.3 + - - -
95A LYS 3.5 2.3 - - - +
97A VAL* 1.3 72.3 - - - +
99A PRO* 1.3 65.4 - - - +
100A LYS* 3.3 13.2 + - - +
101A TYR* 3.0 20.8 + - - -
103A GLY* 2.9 18.7 + - - -
143A ILE* 3.9 13.9 - - - +
312E ILE* 3.5 34.7 + - - +
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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