Contacts of the helix formed by residues 57 - 70 (chain D) in PDB entry 3NJ4
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D HIS* 2.8 17.4 + - + +
56D MET* 1.3 82.4 - - - +
58D VAL* 1.3 59.7 + - - +
59D GLU* 3.3 3.6 + - - -
60D THR* 3.2 14.3 + - - -
61D ALA* 2.9 24.1 + - - +
83D SER 3.5 17.9 - - - +
85D GLN* 3.3 29.2 - - - +
88D ALA* 3.5 6.7 - - - -
347D LEU* 3.7 17.9 - - + -
604D AFX 2.9 25.0 + - - +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ALA* 3.6 21.5 - - + +
22D LEU* 3.4 20.3 - - + +
25D ALA* 3.6 25.6 - - + -
57D THR* 1.3 72.6 - - - +
59D GLU* 1.3 72.2 + - - +
61D ALA* 3.2 11.3 + - - +
62D VAL* 3.2 12.1 + - - +
85D GLN* 2.9 23.0 - - - +
87D HIS* 3.8 18.4 - - - +
88D ALA* 3.4 17.7 - - + +
351D MET* 4.5 4.0 - - + -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 5.8 4.2 - - - +
25D ALA* 4.6 0.3 - - - +
29D MET* 3.8 9.8 - - + +
57D THR* 3.2 9.2 + - - -
58D VAL* 1.3 86.4 + - - +
60D THR* 1.3 61.8 + - - +
62D VAL* 3.1 14.0 + - - +
63D LEU 3.3 7.8 + - - -
85D GLN* 4.4 1.7 + - - -
351D MET 4.2 4.3 - - - +
353D HIS 4.0 5.0 - - - +
354D PRO* 4.9 0.3 - - - +
355D SER* 3.4 42.8 + - - -
358D MET* 3.6 18.2 - - + -
362D PHE* 3.3 24.5 - - + -
604D AFX 3.3 27.3 + - - +
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Residues in contact with THR 60 (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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54D LEU* 3.8 5.8 - - + +
55D HIS 2.5 28.0 + - - +
56D MET* 4.3 2.2 - - + -
57D THR* 3.2 14.0 + - - -
59D GLU* 1.3 77.8 - - - +
61D ALA* 1.3 59.2 + - - +
63D LEU* 3.0 3.8 + - + +
64D ILE* 2.8 38.4 + - + +
76D TRP* 3.5 43.1 - - + +
362D PHE* 3.5 15.1 - - + -
604D AFX 3.7 10.0 - - - -
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Residues in contact with ALA 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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22D LEU* 3.3 30.5 - - + -
56D MET* 3.7 9.8 - - + +
57D THR 2.9 13.8 + - - +
58D VAL* 3.3 2.7 - - - +
59D GLU 3.2 0.2 - - - -
60D THR* 1.3 77.6 - - - +
62D VAL* 1.3 60.8 + - - +
64D ILE* 3.4 1.5 + - - -
65D GLU* 3.1 30.1 + - - +
88D ALA 4.3 3.8 - - - +
92D ILE* 3.6 27.5 - - + +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.1 18.2 - - + +
25D ALA* 4.2 5.6 - - + -
26D GLU* 4.0 26.5 - - + +
29D MET* 3.8 23.3 - - + -
32D LEU* 3.6 22.7 - - + -
33D MET* 4.8 2.2 - - - -
36D ARG* 3.3 17.5 + - - +
58D VAL 3.2 11.0 + - - +
59D GLU 3.1 9.9 + - - +
61D ALA* 1.3 74.8 - - - +
63D LEU* 1.3 57.2 + - - +
65D GLU* 4.9 1.8 - - - +
66D THR* 2.6 35.6 + - - +
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Residues in contact with LEU 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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32D LEU* 3.9 7.6 - - + +
54D LEU* 4.6 0.4 - - + -
59D GLU 3.3 2.0 + - - -
60D THR* 3.0 8.2 + - + +
62D VAL* 1.3 76.9 - - - +
64D ILE* 1.3 68.9 + - - +
66D THR* 2.9 13.7 + - - -
67D LEU* 3.0 27.3 + - + +
76D TRP* 4.1 22.0 - - + -
129D LEU* 4.4 2.9 - - + -
362D PHE* 3.6 55.2 - - + +
365D GLN* 4.3 16.8 - - + -
366D VAL* 3.5 31.0 - - + -
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Residues in contact with ILE 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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56D MET* 3.9 24.0 - - + -
60D THR* 2.8 29.0 + - + +
61D ALA* 3.7 5.6 - - - +
63D LEU* 1.3 72.9 - - - +
65D GLU* 1.3 61.8 + - - +
67D LEU* 3.4 11.2 + - - +
68D VAL* 3.2 21.0 + - - +
74D VAL* 4.1 19.9 - - + +
76D TRP* 3.5 47.1 - - + -
92D ILE* 4.3 10.1 - - + -
97D ILE* 3.8 28.7 - - + -
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Residues in contact with GLU 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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19D ARG* 2.8 47.4 + - - -
22D LEU* 4.3 5.2 - - - +
26D GLU* 4.5 3.5 - - - +
36D ARG* 3.4 21.9 + - - +
61D ALA 3.1 15.5 + - - +
62D VAL* 5.3 1.0 - - - +
64D ILE* 1.3 73.1 - - - +
66D THR* 1.3 59.0 + - - +
68D VAL* 3.3 8.8 + - - +
69D THR* 2.8 33.6 + - - +
92D ILE* 3.7 14.8 - - + -
95D ALA* 3.8 12.3 - - - +
97D ILE* 4.7 6.5 - - + -
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Residues in contact with THR 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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32D LEU* 3.7 32.6 - - + +
35D MET* 4.6 3.8 - - + -
36D ARG* 3.1 26.0 + - + +
62D VAL* 2.6 21.5 + - - +
63D LEU* 2.9 12.4 + - - -
65D GLU* 1.3 74.3 - - - +
67D LEU* 1.3 66.7 + - - +
69D THR* 3.2 2.5 + - - -
70D LEU* 3.1 36.3 + - + +
366D VAL* 4.2 23.6 - - + -
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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
----------------------------------------------------------
45D LEU* 3.8 22.2 - - + -
50D ILE* 3.9 17.0 - - + -
63D LEU* 3.0 24.1 + - + +
64D ILE* 3.6 8.5 - - - +
66D THR* 1.3 75.6 - - - +
68D VAL* 1.3 62.2 - - - +
70D LEU* 3.0 14.4 + - - +
72D ALA* 3.1 24.8 + - + +
74D VAL* 4.1 13.9 - - + -
76D TRP* 3.9 18.4 - - + -
129D LEU* 3.7 23.3 - - + -
366D VAL* 4.4 20.4 - - + -
369D GLN* 4.1 15.7 - - + -
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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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43D LYS* 4.5 2.3 + - - -
64D ILE 3.2 13.9 + - - +
65D GLU* 3.5 9.6 - - - +
66D THR 3.2 0.2 - - - -
67D LEU* 1.3 72.8 - - - +
69D THR* 1.3 55.3 + - - +
70D LEU 2.9 4.5 - - - -
71D GLY* 2.8 27.0 + - - -
72D ALA 3.3 18.8 + - - +
74D VAL* 3.8 16.8 - - + +
97D ILE* 4.0 24.5 - - + -
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Residues in contact with THR 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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36D ARG* 4.0 29.5 + - + -
40D SER* 3.4 29.5 + - - +
43D LYS* 2.7 30.7 + - - +
65D GLU* 2.8 27.2 + - - +
66D THR* 3.2 11.4 + - - -
68D VAL* 1.3 73.6 - - - +
70D LEU* 1.3 58.0 + - + +
71D GLY 3.3 0.7 - - - -
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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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35D MET* 4.1 14.6 - - + +
36D ARG* 4.1 8.1 - - - -
39D TYR* 3.2 37.5 - - + +
43D LYS* 3.4 9.2 - - - -
44D PRO* 4.2 4.0 - - + -
45D LEU* 3.1 35.7 + - + +
66D THR* 3.1 17.3 - - + +
67D LEU 3.0 9.1 + - - +
68D VAL 2.9 1.4 + - - -
69D THR* 1.3 85.6 - - + +
71D GLY* 1.3 54.9 + - - +
72D ALA 3.1 9.0 + - - -
366D VAL* 3.8 29.6 - - + -
370D ILE* 3.9 19.1 - - + -
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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