Contacts of the helix formed by residues 58 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 1.3 75.9 - - - +
59A ASP* 1.3 66.3 + - - +
60A GLU* 3.7 7.4 + - - +
61A GLU* 3.0 43.1 + - - +
62A MET* 2.9 22.1 + - - +
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE 4.0 0.2 + - - -
58A THR* 1.3 71.9 - - - +
60A GLU* 1.3 57.6 + - - +
62A MET* 3.4 22.7 + - - +
63A MET* 3.0 46.2 + - + +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.2 7.6 + - - +
59A ASP* 1.3 77.4 - - - +
61A GLU* 1.3 58.0 + - + +
63A MET* 3.7 15.0 - - + +
64A ILE* 2.9 43.7 + - + +
114A THR* 4.1 22.0 - - - +
115A GLY 4.5 3.3 - - - +
116A ALA* 3.9 25.1 - - + +
117A SER* 4.6 2.6 + - - -
120A SER* 4.8 1.7 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.6 16.9 - - + +
58A THR* 3.0 47.1 + - - +
60A GLU* 1.3 77.3 - - + +
62A MET* 1.3 61.4 + - - +
64A ILE* 3.9 1.9 - - - +
65A LYS* 3.0 24.3 + - - +
117A SER* 2.6 25.0 + - - +
119A LEU* 3.6 27.8 - - - +
120A SER* 3.2 28.7 - - - +
123A LEU* 4.0 13.9 - - + +
355A ARG* 5.2 0.3 + - - -
358A GLU* 4.3 3.5 - - - +
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Residues in contact with MET 62 (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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56A THR* 5.5 4.0 - - + -
57A PHE* 3.1 48.4 - - + +
58A THR 2.9 9.8 + - - +
59A ASP* 3.6 28.0 - - - +
61A GLU* 1.3 76.3 - - - +
63A MET* 1.3 62.4 + - + +
65A LYS* 3.4 7.6 + - - +
66A SER* 3.1 28.4 + - - +
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Residues in contact with MET 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 3.0 42.6 + - + +
60A GLU* 3.7 14.8 - - + +
62A MET* 1.3 76.4 - - + +
64A ILE* 1.3 57.4 + - + +
66A SER* 3.5 6.2 + - - -
67A SER* 3.0 33.2 + - - -
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Residues in contact with ILE 64 (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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60A GLU* 2.9 42.3 + - + +
61A GLU* 3.9 4.3 - - - +
63A MET* 1.3 74.4 - - + +
65A LYS* 1.3 64.3 + - - +
67A SER* 3.3 6.9 + - - -
68A VAL* 3.0 25.9 + - + +
102A LEU* 4.9 4.9 - - + -
105A ILE* 5.1 4.0 - - + -
114A THR* 4.5 9.4 - - + -
116A ALA* 3.7 23.3 - - + -
120A SER* 3.7 15.0 - - - +
123A LEU* 6.2 0.7 - - + -
124A VAL* 3.4 30.7 - - + -
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Residues in contact with LYS 65 (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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57A PHE* 4.1 30.3 - - + -
61A GLU 3.0 18.0 + - - +
62A MET* 3.6 7.4 - - - +
64A ILE* 1.3 78.6 - - - +
66A SER* 1.3 57.9 + - - +
68A VAL* 3.3 3.2 + - - -
69A LYS* 3.0 28.3 + - + +
123A LEU* 4.7 26.2 - - + +
126A GLU* 5.5 3.4 - - - -
127A GLU* 3.4 34.2 - - + +
130A LYS* 4.5 10.3 - - - +
351A TYR* 5.4 4.0 + - - -
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET 3.1 15.5 + - - -
63A MET* 3.7 7.0 - - - -
65A LYS* 1.3 79.3 - - - +
67A SER* 1.3 63.6 + - - +
69A LYS* 3.4 11.5 + - - +
70A LYS* 3.1 22.7 + - - +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.0 19.3 + - - +
64A ILE* 3.6 7.9 - - - -
66A SER* 1.3 76.5 - - - +
68A VAL* 1.3 60.0 + - - +
70A LYS* 3.4 9.1 + - - +
71A PHE* 3.0 27.5 + - - +
100A GLN* 4.3 14.6 + - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.0 17.7 + - + +
65A LYS* 3.8 3.8 - - - +
67A SER* 1.3 73.3 - - - +
69A LYS* 1.3 57.6 + - - +
71A PHE* 3.7 6.2 - - + +
72A ALA* 2.8 33.3 + - - +
100A GLN* 5.9 0.2 - - - +
102A LEU* 3.5 35.7 - - + -
124A VAL* 3.6 18.8 - - + +
127A GLU* 3.9 20.0 - - + -
128A LEU* 3.8 34.8 - - + +
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Residues in contact with LYS 69 (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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65A LYS* 3.0 13.2 + - + +
66A SER* 3.5 13.0 - - - +
68A VAL* 1.3 76.4 - - - +
70A LYS* 1.3 61.5 + - - +
72A ALA* 3.9 3.7 - - - +
73A GLN* 3.1 59.8 + - + +
127A GLU* 3.3 30.1 - - - +
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Residues in contact with LYS 70 (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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66A SER 3.1 10.0 + - - +
67A SER* 3.5 10.8 - - - +
69A LYS* 1.3 77.0 - - - +
71A PHE* 1.3 59.2 + - - +
73A GLN* 3.4 6.4 + - - -
74A GLU* 2.7 75.1 + - + +
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Residues in contact with PHE 71 (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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67A SER 3.0 17.0 + - - +
68A VAL* 3.7 5.8 - - - +
70A LYS* 1.3 76.1 - - - +
72A ALA* 1.3 56.8 + - - +
74A GLU* 4.9 2.0 - - - -
75A GLN* 2.7 63.8 + - + +
76A ILE* 3.5 29.6 + - + -
92A SER 5.5 0.7 - - - -
93A VAL* 4.1 8.7 - - - -
96A GLY* 3.7 35.7 - - - -
97A LEU* 3.8 20.9 - - + -
99A GLN* 5.5 1.1 - - - -
100A GLN* 3.8 28.0 - - + +
102A LEU* 3.9 17.0 - - + -
128A LEU* 4.3 4.7 - - + -
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Residues in contact with ALA 72 (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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68A VAL 2.8 21.6 + - - +
69A LYS* 3.9 4.7 - - - +
71A PHE* 1.3 72.5 - - - +
73A GLN* 1.3 59.1 + - - +
76A ILE* 3.1 28.0 + - + +
77A ALA* 2.9 28.6 + - - +
127A GLU 4.5 8.3 - - - +
128A LEU* 4.4 9.2 - - + -
131A VAL* 3.7 25.0 - - + +
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Residues in contact with GLN 73 (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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69A LYS* 3.1 55.2 + - + +
70A LYS* 3.9 5.2 - - - +
72A ALA* 1.3 76.7 - - - +
74A GLU* 1.3 62.4 + - + +
77A ALA* 3.4 24.2 - - + +
78A PRO* 3.6 5.4 - - - +
131A VAL* 4.9 10.1 - - + -
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Residues in contact with GLU 74 (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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70A LYS* 2.7 62.8 + - + +
71A PHE* 4.2 1.6 - - - +
73A GLN* 1.3 80.5 - - + +
75A GLN* 1.3 79.2 + - + +
78A PRO* 3.7 15.2 - - - +
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Residues in contact with GLN 75 (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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71A PHE* 2.7 53.0 + - + +
74A GLU* 1.3 92.1 + - + +
76A ILE* 1.3 58.9 + - - +
78A PRO* 4.2 2.4 - - - +
79A LEU* 3.6 23.2 - - - +
92A SER* 5.2 6.8 + - - +
93A VAL* 4.0 7.8 - - + +
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Residues in contact with ILE 76 (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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71A PHE* 3.5 32.3 - - + -
72A ALA* 3.1 21.3 + - + +
75A GLN* 1.3 80.4 - - - +
77A ALA* 1.3 67.5 + - - +
78A PRO* 3.3 2.9 - - - -
79A LEU* 2.8 17.7 + - - +
80A VAL* 3.3 15.9 + - + +
83A MET* 4.4 5.6 - - + -
93A VAL* 4.1 13.9 - - + -
128A LEU* 3.5 25.4 - - + +
131A VAL* 3.9 14.4 - - + -
132A ASP* 4.1 3.6 - - + -
135A VAL* 3.8 33.2 - - + -
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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