Contacts of the helix formed by residues 60 - 74 (chain B) in PDB entry 1JLH
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.9 13.8 - - + -
22B GLU* 6.2 0.7 - - - +
23B LEU* 4.1 15.5 - - + -
28B LEU* 4.1 22.7 - - + -
35B ARG* 4.7 2.2 - - - +
39B PHE* 3.7 10.8 - - - -
59B VAL* 1.3 83.4 - - - +
61B GLU* 1.3 65.0 + - - +
62B ASP* 3.4 12.9 + - - +
63B VAL* 3.2 15.9 + - - +
64B MET* 3.1 20.3 + - - +
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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
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32B ASN* 4.3 3.2 + - - +
38B HIS* 3.0 41.8 + - - +
39B PHE* 3.5 21.6 - - + -
60B THR* 1.3 75.7 - - - +
62B ASP* 1.3 67.4 + - - +
64B MET* 3.4 4.3 + - - +
65B ARG* 2.9 24.6 + - - +
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Residues in contact with ASP 62 (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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15B TRP* 4.2 22.3 + - + +
60B THR* 3.2 9.9 + - - +
61B GLU* 1.3 79.9 - - - +
63B VAL* 1.3 58.2 + - - +
65B ARG* 3.0 34.7 + - - +
66B MET* 2.8 36.0 + - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.3 1.6 - - + -
15B TRP* 3.6 44.0 - - + -
59B VAL* 3.2 27.1 - - + -
60B THR* 3.2 12.9 + - - +
62B ASP* 1.3 75.0 - - - +
64B MET* 1.3 59.0 + - - +
66B MET* 3.1 11.9 + - + +
67B LEU* 2.8 45.6 + - + +
325B TRP* 3.7 33.0 - - + -
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Residues in contact with MET 64 (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 PHE* 3.7 18.8 - - + -
54B TYR* 3.6 27.1 - - + +
59B VAL* 3.2 28.7 - - + -
60B THR 3.1 18.2 + - - +
61B GLU* 3.8 6.1 - - - +
63B VAL* 1.3 75.2 - - - +
65B ARG* 1.3 62.4 + - - +
67B LEU* 3.2 13.9 + - + +
68B VAL* 3.0 31.4 + - + +
318B LEU* 4.2 24.2 - - + +
321B LEU* 5.6 2.5 - - + -
322B LEU* 3.9 21.1 - - + -
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Residues in contact with ARG 65 (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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11B LYS* 3.3 27.7 - - - +
61B GLU 2.9 14.8 + - - +
62B ASP* 3.0 43.1 + - - +
64B MET* 1.3 78.1 - - - +
66B MET* 1.3 68.6 + - - +
68B VAL* 3.3 7.1 + - - +
69B ASP* 3.0 40.5 + - - +
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 4.8 4.2 - - - +
11B LYS* 3.8 51.8 - - + +
12B LEU* 3.5 28.1 - - + +
15B TRP* 3.3 49.4 - - + +
62B ASP* 2.8 18.2 + - + +
63B VAL* 3.6 22.7 - - + +
65B ARG* 1.3 79.5 - - - +
67B LEU* 1.3 57.8 + - - +
69B ASP* 3.3 11.1 + - - +
70B LEU* 2.9 26.0 + - - +
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Residues in contact with LEU 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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12B LEU* 3.4 28.7 - - + -
59B VAL* 4.9 0.2 - - + -
63B VAL* 2.8 34.2 + - + +
64B MET* 3.6 24.0 - - + +
66B MET* 1.3 73.7 - - - +
68B VAL* 1.3 60.6 + - - +
70B LEU* 3.0 13.9 + - + +
71B ALA* 2.9 22.0 + - - +
321B LEU* 3.5 55.0 - - + +
322B LEU* 4.7 3.4 - - + +
324B ILE* 5.1 2.7 - - + -
325B TRP* 4.3 19.7 - - + +
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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
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64B MET* 3.0 24.5 + - + +
65B ARG* 3.7 6.3 - - - +
67B LEU* 1.3 73.4 - - - +
69B ASP* 1.3 67.3 + - - +
71B ALA* 3.0 4.9 + - - +
72B LYS* 3.0 46.9 + - - +
311B LEU* 4.0 20.9 - - + +
312B GLU* 4.3 32.5 - - + +
318B LEU* 4.9 5.2 - - + -
321B LEU* 4.0 15.7 - - + -
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Residues in contact with ASP 69 (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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8B GLN* 3.4 25.4 - - - +
11B LYS* 4.7 4.9 + - - -
65B ARG* 3.0 39.1 + - - +
66B MET* 3.5 11.2 - - - +
67B LEU 3.2 0.2 - - - -
68B VAL* 1.3 78.2 - - - +
70B LEU* 1.3 58.5 + - - +
72B LYS* 3.4 21.5 + - - +
73B SER* 2.8 30.8 + - - -
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Residues in contact with LEU 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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3B LEU* 4.1 9.9 - - + -
6B ASP* 4.0 14.4 - - - +
8B GLN* 3.8 6.9 - - + +
9B PHE* 4.2 20.4 - - + +
12B LEU* 3.7 23.3 - - + -
66B MET 2.9 12.6 + - - +
67B LEU* 3.1 14.1 - - + +
69B ASP* 1.3 78.6 - - - +
71B ALA* 1.3 56.6 + - - +
73B SER* 3.3 0.3 + - - -
74B ARG* 2.8 52.3 + - + +
321B LEU* 6.2 1.1 - - + -
324B ILE* 4.2 25.1 - - + -
503B ILE* 4.4 12.3 - - + -
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Residues in contact with ALA 71 (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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67B LEU 2.9 11.2 + - - +
68B VAL* 3.0 12.5 + - - +
70B LEU* 1.3 78.2 - - - +
72B LYS* 1.3 58.5 + - - +
75B GLY 3.4 2.8 + - - -
76B VAL* 3.0 51.4 + - + +
77B GLU 4.9 0.2 + - - -
311B LEU* 4.0 16.3 - - + +
317B VAL* 4.7 4.3 - - + -
321B LEU* 4.3 18.6 - - + -
503B ILE* 4.6 5.5 - - - +
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Residues in contact with LYS 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* 3.0 37.5 + - - +
69B ASP* 3.7 19.0 + - - +
71B ALA* 1.3 73.4 - - - +
73B SER* 1.3 62.0 + - - +
75B GLY* 2.8 21.3 + - - -
76B VAL 5.0 0.7 - - - +
77B GLU* 4.7 9.0 - - - +
311B LEU* 3.6 18.6 - - + -
312B GLU* 5.1 8.5 + - - +
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Residues in contact with SER 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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6B ASP* 2.5 31.7 + - - +
7B PRO* 4.5 4.9 - - - +
8B GLN* 3.4 19.7 + - - +
69B ASP 2.8 18.5 + - - -
70B LEU 3.6 3.6 - - - -
72B LYS* 1.3 77.0 - - - +
74B ARG* 1.3 59.1 + - - +
75B GLY* 3.3 3.3 + - - -
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Residues in contact with ARG 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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2B ALA* 3.9 18.8 + - - +
3B LEU* 4.3 5.6 - - - +
6B ASP* 3.6 25.8 + - - +
70B LEU* 2.8 38.1 + - + +
71B ALA 4.2 2.7 - - - +
72B LYS 3.2 0.2 - - - -
73B SER* 1.3 77.4 + - - +
75B GLY* 1.3 63.3 + - - +
76B VAL* 3.5 1.7 + - + -
502B ILE* 3.0 32.5 + - - +
503B ILE* 2.9 40.9 + - + +
505B ASP* 3.1 36.2 + - - +
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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