Contacts of the helix formed by residues 77 - 92 (chain A) in PDB entry 5JLH
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 ASN 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.2 2.0 - - - +
67A LYS* 4.0 17.1 - - - +
69A PRO* 3.6 8.9 + - + +
75A VAL* 4.7 2.9 - - - +
76A THR* 1.3 86.4 + - - +
78A TRP* 1.3 66.6 + - - +
79A ASP* 2.5 35.9 + - - +
80A ASP* 2.9 29.4 + - + +
81A MET* 3.3 17.2 + - - +
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Residues in contact with TRP 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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75A VAL* 2.9 41.9 + - + +
76A THR 4.7 6.5 - - - -
77A ASN* 1.3 71.5 + - - +
79A ASP* 1.3 69.0 + - - +
80A ASP 3.0 1.6 - - - -
81A MET* 3.0 16.3 + - + +
82A GLU* 2.8 22.7 + - - +
85A TRP* 4.8 4.3 - + - -
113A ALA* 5.1 0.9 - - + -
114A ASN* 3.8 19.5 - - + -
117A LYS* 3.4 48.2 - - + +
118A MET* 3.7 20.0 - - + -
121A ILE* 3.4 32.7 - - + +
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Residues in contact with ASP 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 ARG* 5.3 2.9 + - - -
77A ASN* 2.5 27.1 + - - +
78A TRP* 1.3 76.6 - - - +
80A ASP* 1.3 86.5 + - - +
82A GLU* 3.3 13.5 + - - +
83A LYS* 2.9 38.1 + - - +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.9 20.7 - - + +
36A ARG* 3.1 27.2 + - - -
67A LYS* 4.0 17.0 - - - +
69A PRO* 3.6 16.4 - - + +
77A ASN* 2.9 32.4 + - - +
78A TRP 3.0 0.4 - - - -
79A ASP* 1.3 102.7 + - - +
81A MET* 1.3 61.9 + - - +
83A LYS* 3.0 9.6 + - - +
84A ILE* 2.9 26.1 + - - +
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Residues in contact with MET 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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11A ASN* 3.4 26.7 - - - +
32A SER* 5.6 0.7 - - - -
69A PRO* 4.0 13.6 - - + +
70A ILE* 3.3 40.8 - - + -
75A VAL* 4.2 15.7 - - + -
77A ASN 3.3 10.0 + - - +
78A TRP* 3.0 19.4 + - + +
80A ASP* 1.3 75.0 - - - +
82A GLU* 1.3 66.8 + - - +
84A ILE* 3.0 12.5 + - + +
85A TRP* 2.9 55.3 + - + +
118A MET* 6.2 0.7 - - - -
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Residues in contact with GLU 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 TRP 2.8 12.4 + - - +
79A ASP* 3.5 15.9 - - - +
81A MET* 1.3 76.6 - - - +
83A LYS* 1.3 73.3 + - - +
85A TRP* 3.3 14.5 + - - +
86A HIS* 2.9 43.0 + - - +
121A ILE* 4.8 12.5 - - + +
125A THR* 3.8 28.5 - - + +
126A PHE* 3.8 8.6 - - + -
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Residues in contact with LYS 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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34A VAL* 4.7 4.9 - - + -
36A ARG* 3.4 34.6 - - - +
50A ASP* 3.9 11.5 + - - +
51A SER* 3.9 11.9 - - - +
53A VAL* 4.2 23.7 - - + +
79A ASP* 2.9 25.1 + - - +
80A ASP* 3.0 18.1 + - - +
82A GLU* 1.3 82.5 - - - +
84A ILE* 1.4 58.8 + - - +
86A HIS* 3.2 9.6 + - - +
87A HIS* 2.9 29.3 + - - +
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Residues in contact with ILE 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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11A ASN* 4.7 4.3 - - - +
16A CYS* 3.3 32.1 - - - -
30A PHE* 4.0 12.0 - - + -
32A SER* 3.6 35.9 - - - -
33A ILE 3.8 2.0 - - - +
34A VAL* 4.2 7.0 - - + -
53A VAL* 3.8 20.2 - - + -
69A PRO* 3.6 24.9 - - + -
80A ASP 2.9 14.3 + - - +
81A MET* 3.0 12.8 + - + +
83A LYS* 1.4 77.8 - - - +
85A TRP* 1.3 57.9 + - - +
87A HIS* 3.2 4.7 + - - +
88A THR* 3.0 25.5 + - - +
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Residues in contact with TRP 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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9A ILE* 4.1 21.4 - - + +
11A ASN* 3.1 26.9 - - + +
16A CYS* 4.9 0.2 - - - -
78A TRP* 4.8 2.5 - + - -
81A MET* 2.9 43.8 + - + -
82A GLU* 3.7 4.9 - - - +
84A ILE* 1.3 72.5 - - - +
86A HIS* 1.3 66.3 + - - +
88A THR* 2.5 27.5 + - + -
89A PHE* 2.9 13.8 + + + -
104A LEU* 3.9 30.5 - - + +
118A MET* 3.8 35.4 - - + -
121A ILE* 3.7 31.4 - - + -
122A MET* 3.9 13.7 - - + -
126A PHE* 3.4 29.6 - + + -
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Residues in contact with HIS 86 (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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82A GLU* 2.9 31.2 + - - +
83A LYS* 3.2 13.2 - - - +
85A TRP* 1.3 75.4 - - - +
87A HIS* 1.3 60.9 + - - +
89A PHE* 3.3 0.8 + - - -
90A TYR* 2.9 77.8 + + + +
91A ASN* 5.1 4.8 + - - -
126A PHE* 3.7 12.9 - + + -
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Residues in contact with HIS 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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30A PHE* 3.7 19.9 - + - -
53A VAL* 3.6 39.6 + - + -
54A GLY* 4.2 11.0 - - - -
55A ASP* 4.8 5.5 + - - -
56A GLU* 5.3 6.6 + - - +
83A LYS 2.9 12.6 + - - +
84A ILE 3.4 7.9 - - - +
86A HIS* 1.3 76.5 + - - +
88A THR* 1.3 65.8 + - - +
91A ASN* 2.9 54.0 + - - +
92A GLU* 3.0 49.3 + - - +
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Residues in contact with THR 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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9A ILE* 4.0 13.0 - - + +
16A CYS* 4.2 14.4 - - + -
18A ALA* 4.6 15.3 - - + -
28A ALA* 6.1 0.7 - - - -
30A PHE* 3.4 29.8 - - + -
84A ILE 3.0 16.2 + - - +
85A TRP* 2.5 18.0 + - + +
87A HIS* 1.3 79.6 + - - +
89A PHE* 1.3 91.7 + - - +
92A GLU* 3.4 11.7 + - - +
93A LEU* 3.0 26.7 + - - +
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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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7A LEU* 3.6 21.5 - - + -
9A ILE* 3.7 26.2 - - + -
85A TRP* 2.9 31.1 + - + +
86A HIS* 4.1 2.0 - - - +
88A THR* 1.3 88.2 + - - +
90A TYR* 1.3 63.7 + - + +
93A LEU* 3.5 5.3 - - + -
94A ARG* 2.6 35.7 + - - -
95A VAL* 3.4 31.2 + - + +
97A PRO* 3.7 26.7 - - + -
102A VAL* 4.5 8.3 - - + -
122A MET* 4.2 13.9 - - + -
126A PHE* 3.7 34.1 - + - -
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Residues in contact with TYR 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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86A HIS* 2.9 69.3 + + + +
89A PHE* 1.3 76.7 - - + +
91A ASN* 1.3 70.1 + - - +
94A ARG* 3.7 18.3 + - - +
95A VAL 3.8 22.2 - - - -
96A ALA* 5.1 2.0 - - - -
97A PRO* 4.4 14.9 - - + +
98A GLU* 5.5 1.7 + - - -
126A PHE* 4.7 15.3 - + - +
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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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86A HIS* 5.1 4.8 + - - -
87A HIS* 2.9 60.4 + - + +
90A TYR* 1.3 81.3 + - - +
92A GLU* 1.3 63.2 + - - +
94A ARG* 4.4 12.1 + - - -
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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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28A ALA* 3.4 31.0 - - + -
30A PHE* 4.0 10.3 - - + +
55A ASP* 4.7 6.9 - - - +
87A HIS* 3.0 48.7 + - - +
88A THR* 3.6 9.1 - - - +
91A ASN* 1.3 81.1 - - - +
93A LEU* 1.3 69.1 + - + +
94A ARG* 3.4 11.7 + - - +
424F ARG* 5.9 1.2 + - - -
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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