Contacts of the helix formed by residues 76 - 88 (chain A) in PDB entry 1JG4
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 ALA 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASP* 3.5 13.9 - - - +
64A GLU* 3.6 24.5 - - - -
65A PRO* 3.7 12.4 - - + +
75A SER* 1.3 74.9 - - - +
77A PRO* 1.3 72.3 - - - +
78A HIS* 3.7 20.2 - - + +
79A MET* 3.0 16.9 + - + +
80A VAL* 3.2 10.0 + - - +
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TRP* 4.1 19.7 - - + -
24A THR* 4.5 6.3 - - + -
28A LEU* 4.1 19.3 - - + -
43A PHE* 3.6 12.2 - - + -
48A ARG* 3.6 38.1 - - - +
60A ALA 4.3 0.4 - - - +
62A ILE 4.1 4.5 - - - +
63A ASP* 3.3 21.3 - - - +
75A SER 3.6 0.4 - - - +
76A ALA* 1.3 81.4 - - + +
78A HIS* 1.3 61.3 + - - +
80A VAL 3.3 1.2 + - - -
81A ALA* 3.0 23.4 + - - +
104A TRP* 4.2 11.7 - - + -
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Residues in contact with HIS 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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28A LEU* 3.9 16.5 - - + +
31A GLU* 5.9 0.4 - - - +
33A ILE* 3.7 15.7 - - + +
63A ASP* 2.8 45.6 + - - +
76A ALA* 3.7 18.8 - - + +
77A PRO* 1.3 77.2 - - - +
79A MET* 1.3 75.2 + - + +
81A ALA* 3.4 1.2 + - - +
82A ILE* 2.9 50.8 + - + +
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Residues in contact with MET 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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75A SER* 4.5 10.8 - - - -
76A ALA* 3.0 14.4 + - + +
78A HIS* 1.3 97.6 - - + +
80A VAL* 1.3 67.2 + - - +
82A ILE* 3.4 11.0 + - + +
83A MET* 3.1 33.1 + - - +
198A LEU* 4.5 10.8 - - - -
215A GLY 5.1 0.9 - - - +
216A VAL* 3.4 34.8 - - + -
218A PHE* 3.5 33.2 - - + -
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Residues in contact with VAL 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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43A PHE* 4.1 4.7 - - + -
75A SER* 3.6 26.5 - - - +
76A ALA 3.2 4.1 + - - +
77A PRO 3.7 6.7 - - - +
79A MET* 1.3 77.4 - - - +
81A ALA* 1.3 63.7 + - - +
83A MET* 3.4 7.3 + - - +
84A LEU* 3.0 26.0 + - + +
104A TRP* 3.5 26.7 - - + -
105A ASN* 3.6 24.4 - - + +
108A LEU* 3.6 32.3 - - + -
500A SAM 5.9 1.1 - - - +
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Residues in contact with ALA 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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28A LEU* 4.7 0.9 - - + -
33A ILE* 3.7 19.1 - - + +
34A ILE* 3.8 18.6 - - + -
39A VAL* 4.5 4.2 - - + +
43A PHE* 3.7 21.1 - - + -
77A PRO 3.0 17.6 + - - +
78A HIS* 3.6 4.5 - - - +
80A VAL* 1.3 77.6 - - - +
82A ILE* 1.3 62.9 + - - +
84A LEU* 3.2 3.0 + - - +
85A GLU* 2.9 29.2 + - - +
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Residues in contact with ILE 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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33A ILE* 3.9 26.0 - - + +
78A HIS* 2.9 41.5 + - + +
79A MET* 3.7 13.5 - - + +
80A VAL 3.3 0.2 - - - -
81A ALA* 1.3 75.5 - - - +
83A MET* 1.3 63.8 + - - +
85A GLU* 3.3 5.9 + - - +
86A ILE* 3.0 42.4 + - + +
198A LEU* 4.3 13.9 - - + -
213A HIS* 5.8 2.5 - - + +
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Residues in contact with MET 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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75A SER* 6.4 0.2 - - - -
79A MET* 3.1 24.8 + - - +
80A VAL* 3.9 5.4 - - - +
82A ILE* 1.3 75.9 - - - +
84A LEU* 1.3 59.8 + - + +
86A ILE* 3.4 6.2 + - - +
87A ALA* 3.0 26.5 + - - +
105A ASN* 6.0 2.0 - - - +
163A ILE* 3.9 26.4 - - + +
164A VAL 3.5 25.8 - - - +
165A THR* 4.4 7.4 - - + -
186A ILE* 3.6 26.5 - - + +
198A LEU* 4.1 26.5 - - + -
218A PHE* 3.6 29.8 - - + -
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Residues in contact with LEU 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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39A VAL* 4.0 20.8 - - + +
42A ALA* 5.5 0.7 - - + -
43A PHE* 4.0 20.9 - - + -
80A VAL* 3.0 25.9 + - + +
81A ALA 3.7 3.6 - - - +
83A MET* 1.3 74.1 - - + +
85A GLU* 1.3 66.1 + - - +
87A ALA* 3.1 14.3 + - - +
88A ASN* 3.3 9.7 + - - -
89A LEU* 3.9 19.3 + - + +
105A ASN* 3.8 10.8 - - - +
108A LEU* 4.0 23.8 - - + -
109A ILE* 3.7 31.0 - - + -
112A ILE* 4.6 9.4 - - + +
163A ILE* 4.5 8.3 - - + -
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Residues in contact with GLU 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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33A ILE 3.6 17.3 - - - +
34A ILE* 3.5 2.4 - - - -
35A ARG* 2.7 33.5 + - + +
36A SER* 2.9 32.9 + - - -
39A VAL* 3.4 18.3 - - + +
81A ALA 2.9 21.2 + - - +
82A ILE* 3.8 5.6 - - - +
84A LEU* 1.3 76.3 - - - +
86A ILE* 1.3 64.5 + - + +
88A ASN* 3.2 15.3 + - - +
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Residues in contact with ILE 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 ILE* 3.0 34.1 + - + +
83A MET* 3.7 7.0 - - - +
84A LEU 3.3 0.2 - - - -
85A GLU* 1.3 78.1 - - + +
87A ALA* 1.3 60.9 + - - +
88A ASN* 3.2 2.8 + - - +
184A LYS* 2.9 27.8 + - - +
186A ILE* 3.8 19.7 - - + -
198A LEU* 4.2 12.1 - - + -
200A GLU* 3.7 33.0 - - + +
213A HIS* 3.7 37.5 - - + +
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Residues in contact with ALA 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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83A MET 3.0 14.1 + - - +
84A LEU* 3.1 11.6 + - - +
86A ILE* 1.3 77.6 - - - +
88A ASN* 1.3 68.1 + - - +
89A LEU* 3.2 22.8 + - + -
93A MET* 5.0 1.0 - - - +
161A VAL* 3.8 20.3 - - + +
163A ILE* 4.0 13.2 - - + -
184A LYS* 4.2 9.3 - - - +
186A ILE* 3.6 16.5 - - + +
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Residues in contact with ASN 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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84A LEU 3.3 5.1 + - - -
85A GLU* 3.2 13.1 + - - +
86A ILE 3.2 7.1 - - - +
87A ALA* 1.3 78.8 - - - +
89A LEU* 1.3 63.7 + - - +
90A LYS* 3.8 26.8 + - - +
93A MET* 3.6 15.1 - - - +
184A LYS* 4.8 6.5 - - - +
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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