Contacts of the helix formed by residues 76 - 85 (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 CYS 76 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D CYS* 3.8 21.3 - - - -
36D ILE* 4.1 15.3 - - + -
37D ASN* 3.3 27.8 + - - +
43D PRO* 5.8 0.4 - - + +
72D CYS* 2.9 36.7 + - - +
75D ASN* 1.3 82.0 - - - +
77D GLY* 1.3 67.3 + - - +
79D ARG* 4.0 12.0 - - - +
80D PHE* 3.4 25.7 + - + -
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Residues in contact with GLY 77 (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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72D CYS 4.4 1.8 + - - -
74D LYS 4.6 4.6 + - - -
75D ASN 3.6 1.8 - - - -
76D CYS* 1.3 77.8 - - - +
78D ARG* 1.3 66.2 + - - -
79D ARG* 3.1 1.3 - - - -
80D PHE* 2.8 16.8 + - - +
81D HIS* 3.1 27.8 + - - -
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Residues in contact with ARG 78 (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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77D GLY* 1.3 69.7 - - - -
79D ARG* 1.3 65.0 + - + +
81D HIS* 3.1 28.8 + - - +
82D ASN* 2.9 46.3 + - - +
125D LEU* 3.0 33.3 - - - +
127D GLU* 4.0 24.4 + - - +
128D GLU* 4.3 6.3 + - - -
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Residues in contact with ARG 79 (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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36D ILE 3.1 26.3 + - - -
37D ASN* 3.7 20.8 + - - +
39D GLU 3.2 11.9 + - - -
40D LEU* 3.0 31.1 + - - +
43D PRO* 3.4 31.7 - - + +
44D GLN* 4.7 0.6 - - - +
76D CYS 4.0 11.7 - - - +
77D GLY 2.9 2.6 + - - -
78D ARG* 1.3 75.4 - - + +
80D PHE* 1.3 61.7 + - - +
82D ASN* 3.7 9.6 + - - +
83D GLU* 3.6 22.9 + - - +
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Residues in contact with PHE 80 (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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36D ILE* 4.2 6.7 - - + -
43D PRO* 4.2 17.7 - - + -
46D ALA* 4.1 18.6 - - + -
47D VAL* 3.6 25.8 - - + -
50D LEU* 3.7 18.6 - - + -
69D LEU* 3.8 12.3 - - + -
72D CYS* 3.5 35.0 - - + +
73D MSE 3.8 18.2 - - - -
76D CYS* 3.4 29.4 - - + +
77D GLY 2.8 11.3 + - - +
79D ARG* 1.3 73.4 - - - +
81D HIS* 1.3 65.5 + - - +
83D GLU* 3.1 4.9 + - - +
84D VAL* 3.0 39.4 + - + +
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Residues in contact with HIS 81 (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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72D CYS 4.8 0.2 - - - -
73D MSE 2.8 54.4 + - + +
77D GLY* 3.1 25.8 + - - -
78D ARG* 3.1 47.8 + - - +
80D PHE* 1.3 77.3 - - + +
82D ASN* 1.3 55.9 + - - +
84D VAL* 3.1 8.3 + - - +
85D GLY* 2.9 27.0 + - - -
125D LEU* 3.8 21.4 - - + +
128D GLU* 4.1 7.2 - - - +
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Residues in contact with ASN 82 (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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78D ARG* 2.9 42.4 + - - +
79D ARG* 3.9 8.7 - - - +
80D PHE 3.2 0.4 - - - -
81D HIS* 1.3 75.8 - - - +
83D GLU* 1.3 66.1 + - - +
85D GLY* 3.6 6.1 + - - -
86D LYS* 3.5 23.9 + - - +
128D GLU* 3.5 19.5 - - - +
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Residues in contact with GLU 83 (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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43D PRO* 3.9 4.0 - - + +
44D GLN* 3.6 47.9 - - + +
47D VAL* 3.9 24.6 - - + +
79D ARG 3.6 13.0 + - - +
80D PHE 3.1 8.5 + - - +
82D ASN* 1.3 78.0 - - - +
84D VAL* 1.3 65.4 + - - +
86D LYS* 3.1 45.9 + - - +
88D ARG* 4.0 9.4 + - - +
89D PHE* 3.6 15.1 - - - +
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Residues in contact with VAL 84 (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* 4.2 6.1 - - + -
69D LEU* 4.7 2.0 - - + -
73D MSE 3.7 19.3 - - + -
80D PHE* 3.0 45.8 + - + +
81D HIS* 3.1 7.8 + - - +
83D GLU* 1.3 75.0 - - - +
85D GLY* 1.3 57.7 + - - +
86D LYS 2.9 11.1 + - - +
89D PHE* 3.5 24.0 - - + -
90D LEU* 3.5 18.6 - - + +
121D TRP* 3.8 34.8 - - + -
131D ILE* 4.4 6.3 - - + -
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Residues in contact with GLY 85 (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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81D HIS 2.9 10.9 + - - -
82D ASN 3.6 2.0 + - - -
83D GLU 3.3 0.8 - - - -
84D VAL* 1.3 75.7 - - - +
86D LYS* 1.3 61.9 + - - +
90D LEU* 4.4 1.1 - - - -
128D GLU* 3.4 24.3 - - - +
130D LYS* 3.4 27.9 - - - +
131D ILE* 3.9 19.7 - - - +
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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