Contacts of the helix formed by residues 76 - 85 (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 CYS 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A CYS* 3.7 24.9 - - - -
36A ILE* 4.2 12.8 - - + -
37A ASN* 3.4 20.6 - - - +
72A CYS* 2.9 38.3 + - - +
74A LYS 3.9 0.2 - - - -
75A ASN* 1.3 82.9 - - - +
77A GLY* 1.3 66.5 + - - +
79A ARG* 3.2 24.7 - - + +
80A PHE* 3.3 19.3 - - + +
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Residues in contact with GLY 77 (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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72A CYS 4.5 0.8 + - - -
73A MSE 4.7 3.8 + - - -
74A LYS 5.3 1.0 - - - -
75A ASN 3.7 2.2 - - - -
76A CYS* 1.3 76.4 - - - +
78A ARG* 1.3 67.7 + - - -
79A ARG* 3.2 1.8 - - - -
80A PHE* 2.9 12.8 + - - +
81A HIS* 3.0 24.0 + - - -
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Residues in contact with ARG 78 (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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77A GLY* 1.3 71.0 - - - -
79A ARG* 1.3 56.0 + - - +
81A HIS* 2.9 17.2 + - + -
82A ASN* 2.7 61.3 + - - +
127A GLU* 6.3 2.1 - - + +
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Residues in contact with ARG 79 (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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36A ILE* 2.9 31.1 + - - +
37A ASN* 4.0 14.7 + - - +
39A GLU 3.2 18.6 + - - -
40A LEU* 3.2 21.8 + - - +
43A PRO* 3.7 25.2 - - + +
76A CYS 3.2 19.7 - - - +
77A GLY* 4.6 0.7 - - - -
78A ARG* 1.3 78.1 - - - +
80A PHE* 1.3 60.2 + - - +
82A ASN* 3.8 8.5 + - - +
83A GLU* 3.6 22.3 + - - +
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Residues in contact with PHE 80 (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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36A ILE* 4.4 6.5 - - + -
43A PRO* 4.2 19.7 - - + -
46A ALA* 4.2 17.7 - - + -
47A VAL* 3.7 25.8 - - + -
50A LEU* 4.0 13.5 - - + -
69A LEU* 4.1 5.2 - - + -
72A CYS* 3.3 41.3 - - + +
73A MSE 3.6 29.2 - - - -
76A CYS* 3.3 29.6 - - + +
77A GLY 2.9 6.2 + - - +
79A ARG* 1.3 79.5 - - + +
81A HIS* 1.3 66.9 + - - +
83A GLU* 2.9 14.9 + - - +
84A VAL* 3.2 17.5 + - + +
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Residues in contact with HIS 81 (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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72A CYS 4.9 0.2 - - - -
73A MSE 2.7 52.5 + - + +
77A GLY* 3.0 22.4 + - - -
78A ARG* 2.9 18.3 + - + +
80A PHE* 1.3 75.8 - - - +
82A ASN* 1.3 58.8 + - - +
84A VAL* 3.2 8.6 + - - +
85A GLY 2.9 24.9 + - - -
125A LEU* 3.9 29.8 - - + +
127A GLU* 5.1 4.3 - - - +
128A GLU* 3.5 22.2 - - - +
131A ILE* 5.4 0.2 - - - +
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Residues in contact with ASN 82 (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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78A ARG* 2.7 49.0 + - - +
79A ARG* 3.9 9.4 + - - +
80A PHE 3.1 0.2 - - - -
81A HIS* 1.3 73.8 - - - +
83A GLU* 1.3 60.4 + - - +
85A GLY* 3.7 5.9 + - - -
86A LYS* 3.1 28.8 + - - +
127A GLU* 5.9 2.6 - - - +
128A GLU* 3.2 26.8 + - - +
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Residues in contact with GLU 83 (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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43A PRO* 3.6 32.8 - - + +
44A GLN* 3.9 23.5 + - - +
47A VAL* 4.0 23.6 - - + +
79A ARG 3.6 6.4 - - - +
80A PHE 2.9 8.4 + - - +
82A ASN* 1.3 77.2 - - - +
84A VAL* 1.3 64.6 + - - +
85A GLY 3.2 2.1 + - - -
86A LYS* 3.2 31.9 + - - +
88A ARG* 2.8 31.2 + - - -
89A PHE* 3.7 10.7 - - - +
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Residues in contact with VAL 84 (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* 4.0 12.1 - - + -
69A LEU* 4.4 3.6 - - + -
73A MSE 3.8 16.4 - - + -
80A PHE* 3.2 35.9 + - + +
81A HIS 3.2 7.1 + - - +
83A GLU* 1.3 76.0 - - - +
85A GLY* 1.3 57.6 + - - +
86A LYS 3.1 5.4 + - - +
89A PHE* 3.6 32.1 - - + -
90A LEU* 3.2 20.9 - - + +
121A TRP* 3.6 28.9 - - + -
131A ILE* 4.4 4.3 - - + -
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Residues in contact with GLY 85 (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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81A HIS 2.9 10.4 + - - -
82A ASN 3.7 2.4 + - - -
83A GLU 3.2 1.0 - - - -
84A VAL* 1.3 75.3 - - - +
86A LYS* 1.3 61.5 + - - +
90A LEU* 4.0 1.1 - - - -
128A GLU* 3.6 31.1 - - - +
130A LYS* 3.1 31.0 + - - +
131A ILE* 4.0 9.6 - - - -
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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