Contacts of the helix formed by residues 60 - 74 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D TRP* 4.1 10.0 - - + -
23D LEU* 4.0 17.9 - - + -
28D LEU* 4.3 16.6 - - + -
35D ARG* 4.9 1.6 - - - +
39D PHE* 3.8 10.3 - - - -
59D VAL* 1.3 79.9 - - - +
61D GLU* 1.3 66.2 + - - +
62D ASP* 3.4 11.3 + - - +
63D VAL* 3.1 22.8 + - - +
64D MET* 3.0 23.7 + - - +
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Residues in contact with GLU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D HIS* 3.8 32.0 + - - +
39D PHE* 3.7 21.9 - - + -
60D THR* 1.3 75.2 - - - +
62D ASP* 1.3 58.4 + - - +
64D MET* 3.4 5.8 + - - +
65D ARG* 2.9 29.7 + - - +
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Residues in contact with ASP 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP* 4.5 18.8 - - + +
60D THR* 3.2 9.4 + - - +
61D GLU* 1.3 80.4 - - - +
63D VAL* 1.3 56.7 + - - +
65D ARG* 3.0 35.3 + - - +
66D MET* 2.9 37.3 + - + +
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Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.6 1.8 - - + -
15D TRP* 3.4 37.7 - - + -
23D LEU* 4.9 0.4 - - + -
59D VAL* 4.1 12.6 - - + -
60D THR* 3.1 29.5 + - - +
62D ASP* 1.3 76.4 - - - +
64D MET* 1.3 59.1 + - - +
66D MET* 3.0 10.0 + - - +
67D LEU* 2.8 43.9 + - + +
325D TRP* 3.8 33.4 - - + -
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D PHE* 3.7 22.2 - - + -
54D TYR* 4.0 20.2 - - + +
59D VAL* 3.7 29.8 - - + -
60D THR 3.0 17.4 + - - +
61D GLU* 3.8 10.3 - - - +
63D VAL* 1.3 74.8 - - - +
65D ARG* 1.3 56.4 + - - +
67D LEU* 3.3 18.6 + - + +
68D VAL* 2.9 37.6 + - + +
318D LEU* 4.0 28.5 - - + +
321D LEU* 5.4 1.6 - - + -
322D LEU* 4.2 15.5 - - + -
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LYS* 3.2 31.7 - - - +
61D GLU 2.9 18.1 + - - +
62D ASP* 3.0 31.3 + - - +
63D VAL 3.1 0.2 - - - -
64D MET* 1.3 76.7 - - - +
66D MET* 1.3 71.3 + - - +
68D VAL* 3.3 7.7 + - - +
69D ASP* 2.9 47.8 + - - +
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Residues in contact with MET 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN* 4.8 3.5 - - - +
11D LYS* 3.9 41.1 - - + +
12D LEU* 3.5 27.2 - - + +
15D TRP* 3.3 52.3 - - + -
62D ASP* 2.9 25.6 + - + +
63D VAL* 3.6 11.7 - - - +
65D ARG* 1.3 89.0 - - - +
67D LEU* 1.3 65.7 + - - +
69D ASP* 3.2 10.2 + - - +
70D LEU* 3.0 21.1 + - - +
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.6 29.8 - - + -
59D VAL* 4.9 2.0 - - + -
63D VAL* 2.8 34.5 + - + +
64D MET* 3.6 24.2 - - + +
66D MET* 1.3 76.8 - - - +
68D VAL* 1.3 61.8 + - - +
70D LEU* 3.0 19.1 + - + +
71D ALA 3.1 9.0 + - - -
321D LEU* 3.6 55.9 - - + +
322D LEU* 4.7 2.2 - - - +
324D ILE* 5.3 2.2 - - + -
325D TRP* 4.2 22.0 - - + +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D MET* 2.9 23.4 + - + +
65D ARG* 3.6 8.1 - - - +
67D LEU* 1.3 75.2 - - - +
69D ASP* 1.3 64.5 + - - +
71D ALA* 3.1 13.3 + - - +
72D LYS* 3.1 40.0 + - - +
311D LEU* 4.1 13.0 - - + -
312D GLU* 4.0 40.8 - - + +
318D LEU* 4.7 5.8 - - + -
321D LEU* 4.0 16.2 - - + -
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN* 3.6 18.9 - - + +
11D LYS* 4.5 6.5 + - + +
65D ARG* 2.9 48.1 + - - +
66D MET* 3.2 11.8 + - - +
68D VAL* 1.3 77.9 - - - +
70D LEU* 1.3 57.5 + - - +
72D LYS* 3.3 21.2 + - - +
73D SER* 2.9 30.1 + - - -
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.2 9.9 - - + -
6D ASP* 3.4 22.0 - - - +
8D GLN* 3.8 6.9 - - + +
9D PHE* 4.2 16.6 - - + +
12D LEU* 4.0 22.7 - - + -
66D MET 3.0 11.8 + - - +
67D LEU* 3.0 13.7 + - + +
69D ASP* 1.3 74.5 - - - +
71D ALA* 1.3 56.1 + - - +
73D SER* 3.1 0.9 + - - -
74D ARG* 2.7 55.8 + - + +
321D LEU* 5.8 1.3 - - + -
324D ILE* 4.4 13.9 - - + -
503D ILE* 4.0 25.4 - - + -
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU 3.1 7.8 + - - +
68D VAL* 3.1 12.2 + - - +
70D LEU* 1.3 79.7 - - - +
72D LYS* 1.3 60.5 - - - +
74D ARG* 3.4 0.4 + - - -
75D GLY 3.2 4.3 + - - -
76D VAL* 3.0 48.1 + - + +
311D LEU* 4.1 15.3 - - + -
317D VAL* 4.6 7.2 - - + -
321D LEU* 4.2 17.6 - - + +
503D ILE* 4.7 5.2 - - - -
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D VAL* 3.1 33.2 + - + +
69D ASP* 3.6 19.7 + - - +
71D ALA* 1.3 75.3 - - - +
73D SER* 1.3 59.4 + - - +
75D GLY* 2.9 21.0 + - - -
76D VAL 5.0 0.9 - - - +
77D GLU* 5.4 5.8 - - - +
311D LEU* 3.5 20.2 - - + -
312D GLU* 4.6 11.7 + - - +
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ASP* 2.6 24.1 + - - +
7D PRO* 4.5 1.2 - - - +
8D GLN* 2.6 37.4 + - - -
69D ASP 2.9 16.6 + - - -
70D LEU 3.4 3.8 - - - -
72D LYS* 1.3 78.9 - - - +
74D ARG* 1.3 63.8 + - - +
75D GLY 3.2 1.1 + - - -
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ALA* 3.7 19.4 + - - +
3D LEU* 4.3 6.0 - - - +
6D ASP* 3.5 27.6 + - - -
70D LEU* 2.7 38.8 + - + +
71D ALA 4.0 3.6 - - - +
72D LYS 3.2 0.2 - - - -
73D SER* 1.3 74.6 + - - +
75D GLY* 1.3 62.5 + - - +
76D VAL* 3.5 1.6 - - + -
502D ILE* 3.4 23.3 + - - +
503D ILE* 2.9 40.3 + - + +
505D ASP* 3.0 45.3 + - - +
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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