Contacts of the helix formed by residues 58 - 76 (chain B) in PDB entry 2JIF
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 THR 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE* 1.3 77.7 - - - +
59B ASP* 1.3 66.1 + - - +
60B GLU* 3.8 6.6 + - - +
61B GLU* 3.1 39.6 + - - +
62B MET* 3.0 21.9 + - - +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE 3.9 0.5 + - - +
58B THR* 1.3 73.3 - - - +
60B GLU* 1.3 56.4 + - - +
62B MET* 3.3 26.2 + - + +
63B MET* 3.0 40.0 + - + +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 3.2 7.2 + - - +
59B ASP* 1.3 79.2 - - - +
61B GLU* 1.3 58.2 + - + +
63B MET* 3.2 8.7 + - + +
64B ILE* 2.9 51.1 + - + +
114B THR* 5.0 9.2 - - - +
115B GLY 4.2 4.6 - - - +
116B ALA* 3.6 28.6 - - + +
117B SER 4.6 1.4 + - - -
120B SER* 5.1 1.2 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.5 15.8 - - + +
58B THR* 3.1 40.9 + - - +
60B GLU* 1.3 77.1 - - + +
62B MET* 1.3 57.5 + - - +
64B ILE* 3.5 3.1 + - - +
65B LYS* 3.0 29.3 + - - +
117B SER* 2.7 24.2 + - - +
119B LEU* 3.8 23.9 - - - +
120B SER* 3.2 29.8 - - - +
123B LEU* 3.9 16.3 - - + +
355B ARG* 5.1 2.3 + - - -
358B GLU* 4.4 3.5 - - - +
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.0 30.7 - - + +
58B THR 3.0 13.9 + - - +
59B ASP* 3.3 37.5 - - + +
61B GLU* 1.3 72.5 - - - +
63B MET* 1.3 61.1 + - + +
65B LYS* 3.5 7.2 + - - +
66B SER* 3.0 29.9 + - - -
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Residues in contact with MET 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP* 3.0 27.0 + - + +
60B GLU* 3.2 8.3 + - + +
62B MET* 1.3 74.2 - - + +
64B ILE* 1.3 66.9 + - + +
66B SER* 3.3 5.8 + - - -
67B SER* 3.0 25.6 + - - -
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 2.9 32.1 + - + +
61B GLU* 3.9 3.8 - - - +
63B MET* 1.3 75.5 - - + +
65B LYS* 1.3 65.1 + - - +
67B SER* 3.1 9.7 + - - +
68B VAL* 3.0 30.3 + - + +
102B LEU* 4.9 5.8 - - + -
105B ILE* 5.1 3.4 - - + -
114B THR* 5.0 10.3 - - + -
116B ALA* 3.7 21.5 - - + -
120B SER* 3.7 28.0 - - - +
123B LEU* 6.3 0.7 - - + -
124B VAL* 3.5 30.7 - - + -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.6 19.2 - - + -
61B GLU 3.0 18.8 + - - +
62B MET* 3.8 5.8 - - - +
64B ILE* 1.3 77.1 - - - +
66B SER* 1.3 59.1 + - - +
68B VAL* 3.4 4.2 + - - +
69B LYS* 3.0 29.1 + - - +
123B LEU* 4.6 31.4 - - + +
126B GLU* 5.7 3.1 + - - -
127B GLU* 3.0 39.6 - - + +
130B LYS* 4.4 8.0 - - - +
351B TYR* 5.2 5.4 + - - -
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Residues in contact with SER 66 (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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62B MET 3.0 18.8 + - - -
63B MET* 3.7 6.5 - - - -
64B ILE 3.2 0.2 - - - -
65B LYS* 1.3 78.6 - - - +
67B SER* 1.3 60.7 + - - +
69B LYS* 3.5 9.2 + - - +
70B LYS* 3.2 21.0 + - - +
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Residues in contact with SER 67 (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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63B MET 3.0 14.5 + - - -
64B ILE* 3.1 14.6 + - - +
66B SER* 1.3 73.9 - - - +
68B VAL* 1.3 65.5 + - - +
70B LYS* 3.4 8.9 + - - +
71B PHE* 3.0 28.6 + - - +
100B GLN* 4.4 13.2 + - - +
102B LEU* 5.7 1.2 - - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.0 23.0 + - + +
65B LYS* 3.8 5.2 - - - +
67B SER* 1.3 75.1 - - - +
69B LYS* 1.3 60.5 + - - +
71B PHE* 3.3 7.1 + - + +
72B ALA* 2.8 29.3 + - + +
100B GLN* 5.8 0.2 - - - -
102B LEU* 3.7 32.3 - - + -
124B VAL* 3.8 22.0 - - + +
127B GLU* 3.6 25.1 - - + -
128B LEU* 3.8 26.7 - - + +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LYS* 3.0 15.6 + - - +
66B SER* 3.6 9.9 - - - +
68B VAL* 1.3 76.5 - - - +
70B LYS* 1.3 62.3 + - - +
72B ALA* 3.7 5.3 - - - +
73B GLN* 3.1 53.1 + - + +
127B GLU* 3.5 26.2 + - - +
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Residues in contact with LYS 70 (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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66B SER 3.2 11.0 + - - +
67B SER* 3.6 11.2 - - - +
68B VAL 3.3 0.2 - - - -
69B LYS* 1.3 79.6 - - - +
71B PHE* 1.3 62.2 + - - +
73B GLN* 3.3 6.2 + - - -
74B GLU* 3.0 67.8 + - - +
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Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER 3.0 17.0 + - - +
68B VAL* 3.7 5.6 - - - +
70B LYS* 1.3 76.2 - - - +
72B ALA* 1.3 59.6 + - - +
74B GLU* 5.0 2.2 - - - -
75B GLN* 2.8 69.0 + - + +
76B ILE* 3.7 24.9 + - + -
92B SER 5.5 0.7 - - - -
93B VAL* 4.1 8.5 - - - -
96B GLY* 3.6 35.9 - - - -
97B LEU* 3.8 20.2 - - + -
100B GLN* 3.7 27.1 - - + +
102B LEU* 4.1 16.8 - - + -
128B LEU* 4.4 3.1 - - + -
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Residues in contact with ALA 72 (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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68B VAL 2.8 20.5 + - - +
69B LYS* 3.7 7.2 - - - +
70B LYS 3.2 0.2 - - - -
71B PHE* 1.3 74.8 - - - +
73B GLN* 1.3 57.3 + - - +
76B ILE* 3.1 25.3 + - + +
77B ALA* 2.9 28.2 + - - +
127B GLU 4.5 10.1 - - - +
128B LEU* 4.6 6.7 - - + -
131B VAL* 3.8 25.7 - - + +
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Residues in contact with GLN 73 (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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69B LYS* 3.1 51.9 + - - +
70B LYS* 3.3 4.8 + - - +
72B ALA* 1.3 77.5 - - - +
74B GLU* 1.3 64.5 + - + +
77B ALA* 3.6 22.4 - - + +
78B PRO* 3.8 6.4 - - - +
131B VAL* 4.7 13.0 - - + +
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Residues in contact with GLU 74 (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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70B LYS* 3.0 59.3 + - + +
71B PHE* 4.3 2.1 - - - +
73B GLN* 1.3 81.7 - - + +
75B GLN* 1.3 75.0 + - + +
78B PRO* 3.7 15.5 - - - +
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Residues in contact with GLN 75 (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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71B PHE* 2.8 47.2 + - + +
74B GLU* 1.3 90.4 - - + +
76B ILE* 1.3 60.1 + - + +
78B PRO* 4.0 2.8 - - - +
79B LEU* 3.6 23.6 - - - +
92B SER* 5.1 16.9 + - - +
93B VAL* 4.1 6.1 - - + +
96B GLY* 6.2 0.6 - - - -
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Residues in contact with ILE 76 (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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71B PHE* 3.7 30.3 - - + -
72B ALA* 3.1 21.5 + - + +
75B GLN* 1.3 80.8 - - - +
77B ALA* 1.3 57.3 + - - +
78B PRO* 3.2 3.1 - - - -
79B LEU* 2.8 28.6 + - - +
80B VAL* 3.3 15.3 + - + -
83B MET* 4.4 6.1 - - + -
93B VAL* 4.2 13.5 - - + -
128B LEU* 3.8 15.9 - - + +
131B VAL* 3.8 14.8 - - + -
132B ASP* 4.1 3.4 - - + -
135B VAL* 3.7 42.6 - - + -
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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