Contacts of the helix formed by residues 87 - 96 (chain B) in PDB entry 1JEQ
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 ASP 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL* 4.4 9.6 - - - +
81B ARG* 2.7 30.9 + - - +
84B MET* 5.1 3.8 - - - +
85B LEU 4.1 4.5 - - - +
86B PRO* 1.3 74.2 - - - +
88B PHE* 1.3 62.9 + - + +
89B ASP* 3.1 16.3 + - - +
90B LEU* 3.0 32.4 + - - +
91B LEU* 3.3 8.0 + - - +
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A TYR* 3.4 33.2 - + + -
325A ARG* 3.2 56.5 - - + +
327A ILE* 4.3 5.2 - - + -
46B VAL* 4.2 9.9 - - + -
47B PHE* 3.5 30.5 - + - -
87B ASP* 1.3 74.9 - - + +
89B ASP* 1.3 61.8 + - - +
91B LEU* 3.0 18.1 + - + +
92B GLU* 2.8 32.3 + - - +
495B LEU* 4.2 5.2 - - + -
498B ALA* 3.9 27.1 - - + -
499B LEU* 4.7 6.1 - - + +
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Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 4.6 11.1 + - - -
81B ARG* 4.3 6.7 - - - +
87B ASP* 3.1 14.9 + - - +
88B PHE* 1.3 78.7 - - - +
90B LEU* 1.3 57.7 + - - +
92B GLU* 4.0 10.1 - - - +
93B ASP* 2.8 34.0 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 5.7 0.7 - - + -
42B VAL* 3.6 34.8 - - + -
54B ILE* 4.8 13.2 - - + +
56B LEU* 4.4 21.5 - - + -
80B HIS* 4.6 7.6 - - + +
81B ARG* 3.7 51.6 - - + +
86B PRO* 4.2 13.2 - - + -
87B ASP* 3.0 16.3 + - - +
89B ASP* 1.3 77.8 - - - +
91B LEU* 1.3 64.9 + - - +
93B ASP* 3.2 5.0 + - - +
94B ILE* 3.1 32.0 + - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 4.5 8.5 - - + +
42B VAL* 3.2 35.9 - - + -
43B GLN* 3.8 15.0 - - + +
46B VAL* 4.2 19.5 - - + -
47B PHE* 4.7 4.9 - - + -
87B ASP 3.8 3.8 - - - +
88B PHE* 3.0 26.8 + - + +
90B LEU* 1.3 78.0 - - - +
92B GLU* 1.3 63.6 + - - +
94B ILE* 3.0 17.7 + - + +
95B GLU* 3.2 17.7 + - - +
495B LEU* 3.7 43.7 - - + +
499B LEU* 4.8 0.7 - - - -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 5.8 0.2 + - - -
88B PHE 2.8 19.2 + - - +
89B ASP* 4.3 10.4 - - - +
91B LEU* 1.3 73.2 - - - +
93B ASP* 1.3 65.9 + - - +
95B GLU* 4.7 0.9 - - - +
96B SER* 3.2 35.2 + - - -
97B LYS* 3.9 0.7 + - - +
499B LEU* 3.9 43.4 - - + +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B HIS* 2.8 37.1 + - + +
81B ARG* 4.9 5.5 + - - -
89B ASP* 2.8 22.1 + - - +
90B LEU* 3.2 12.8 + - + +
91B LEU 3.1 0.8 - - - -
92B GLU* 1.3 82.5 - - - +
94B ILE* 1.3 59.2 + - - +
96B SER 3.4 1.9 - - - +
97B LYS* 3.5 31.7 + - + +
98B ILE* 2.9 33.6 + - + +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 6.3 0.2 - - + -
14B MET* 5.9 4.7 - - - -
31B PHE* 5.7 0.2 - - - -
35B LYS* 2.8 36.5 - - + +
38B ILE* 4.1 28.5 - - + -
39B THR* 3.4 26.0 - - + +
42B VAL* 5.3 4.7 - - + -
56B LEU* 3.6 31.2 - - + -
90B LEU* 3.1 26.0 - - + +
91B LEU* 3.0 11.7 + - + +
93B ASP* 1.3 76.2 - - - +
95B GLU* 1.3 62.9 - - + +
96B SER 4.1 0.9 - - - +
98B ILE* 4.1 14.1 - - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 2.9 32.2 + - - +
39B THR* 5.5 8.7 - - + +
91B LEU 3.2 13.5 + - - +
92B GLU* 4.1 3.4 - - - +
94B ILE* 1.3 76.5 - - + +
96B SER* 1.3 72.8 + - - +
98B ILE 4.0 1.0 - - - +
495B LEU* 4.3 17.5 - - + +
496B HIS* 6.0 2.8 - - - -
499B LEU* 3.1 27.3 - - + +
500B HIS* 3.7 18.0 + - - -
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLU* 3.2 19.9 + - - -
93B ASP 3.4 1.5 - - - +
95B GLU* 1.3 90.6 - - - +
97B LYS* 1.3 73.7 + - - +
98B ILE 2.8 11.9 + - - +
99B GLN* 4.7 3.8 - - - +
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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