Contacts of the helix formed by residues 52 - 68 (chain D) in PDB entry 1N34
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 SER 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A C 5.8 0.7 - - - -
508A C 6.0 0.2 - - - -
509A A 3.5 26.7 - - - -
50D ARG* 3.8 2.2 + - - +
51D PRO* 1.3 72.3 - - - +
53D ASP* 1.3 55.9 + - - +
54D TYR* 2.3 25.9 + - - +
55D ALA* 2.7 35.5 + - - +
56D VAL* 2.8 15.4 - - - +
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Residues in contact with ASP 53 (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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8A A 5.8 4.1 - - + +
51D PRO 3.8 2.8 + - - +
52D SER* 1.3 68.9 - - - +
54D TYR* 1.3 55.1 + - - +
56D VAL* 3.8 9.3 - - - +
57D ARG* 3.0 43.6 + - - +
9E LYS* 3.9 23.6 + - - -
104E ALA* 4.3 17.8 - - + +
107E ARG* 4.0 21.9 + - - +
108E ALA* 5.6 0.9 + - - +
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Residues in contact with TYR 54 (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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8A A 5.8 8.7 - - - +
508A C 3.8 44.0 - - - +
509A A 3.8 27.1 + + - -
52D SER* 2.3 21.6 + - - +
53D ASP* 1.3 67.7 - - - +
55D ALA* 1.3 56.3 + - - +
56D VAL 3.0 1.1 - - - -
57D ARG* 2.6 8.3 + - + -
58D LEU* 2.4 45.9 + - + +
206D PHE* 3.5 39.3 - + - -
209D ARG* 4.7 26.2 - - - +
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Residues in contact with ALA 55 (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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509A A 3.9 23.6 - - - +
51D PRO* 4.8 6.1 - - + -
52D SER* 2.7 30.2 + - - +
54D TYR* 1.3 72.1 - - - +
56D VAL* 1.3 55.8 + - - +
58D LEU* 2.6 18.4 + - + -
59D ARG* 2.5 45.4 + - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PRO* 3.8 22.2 - - + +
52D SER 2.8 24.9 - - - +
53D ASP* 3.8 13.5 - - - +
55D ALA* 1.3 78.2 - - - +
57D ARG* 1.3 74.3 + - - +
59D ARG* 4.0 4.2 - - - +
60D GLU* 3.1 24.0 + - - +
202D LEU* 4.1 17.5 - - + -
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Residues in contact with ARG 57 (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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8A A 5.3 5.8 - - - +
53D ASP* 3.0 39.7 + - - +
54D TYR* 2.6 14.4 + - + +
56D VAL* 1.3 88.0 - - - +
58D LEU* 1.3 67.4 + - - +
60D GLU* 3.3 6.1 + - - +
61D LYS* 2.9 15.9 + - - +
202D LEU* 3.7 24.0 - - + +
203D VAL* 5.4 0.2 - - - -
205D GLU* 2.5 35.8 + - + +
206D PHE* 3.4 44.8 - - + +
9E LYS* 5.0 4.2 - - - +
107E ARG* 3.0 35.6 - - - +
111E GLU* 3.0 17.6 + - - -
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Residues in contact with LEU 58 (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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509A A 3.1 49.8 - - - +
544A G 4.6 13.9 - - - +
545A C 5.6 0.7 - - - +
54D TYR* 2.4 35.9 + - + +
55D ALA* 2.6 13.1 + - - +
57D ARG* 1.3 76.4 - - - +
59D ARG* 1.3 71.5 - - + +
61D LYS* 2.6 14.4 + - - +
62D GLN* 2.7 36.4 + - + +
206D PHE* 3.2 28.0 - - + -
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Residues in contact with ARG 59 (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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509A A 5.4 5.0 + - - -
543A C 3.7 7.3 + - - -
544A G 2.6 27.5 + - - -
14D ARG* 4.1 24.3 + - - +
15D GLU* 2.5 40.5 + - - +
55D ALA* 2.5 28.8 + - + +
56D VAL* 4.0 4.5 - - - +
58D LEU* 1.3 84.5 - - - +
60D GLU* 1.3 52.0 + - - +
62D GLN* 2.4 48.8 + - - +
63D LYS* 2.4 18.4 + - - +
66D ARG* 3.4 16.4 - - - +
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Residues in contact with GLU 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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15D GLU* 4.3 0.2 + - - -
56D VAL 3.1 17.3 + - - +
57D ARG 3.4 3.6 - - - +
59D ARG* 1.3 77.4 - - - +
61D LYS* 1.3 62.9 + - - +
63D LYS* 3.0 27.1 + - - +
64D LEU 3.0 19.4 + - - -
197D PRO 4.0 0.9 - - - +
198D VAL* 3.1 18.4 - - + +
199D ASN* 2.4 43.0 + - + +
202D LEU* 3.6 34.0 - - + +
203D VAL* 4.4 2.2 - - - +
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Residues in contact with LYS 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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545A C 4.0 2.2 - - - -
57D ARG 2.9 9.8 + - - +
58D LEU* 2.6 22.2 + - - +
60D GLU* 1.3 70.0 - - - +
62D GLN* 1.3 113.9 + - - +
63D LYS 2.9 0.5 + - - -
64D LEU* 3.1 1.7 + - - +
65D ARG* 2.7 45.4 + - - +
72D GLU* 3.2 15.9 + - - +
75D PHE* 4.3 5.3 - - + -
203D VAL* 4.0 19.0 - - + +
206D PHE* 3.8 22.2 - - + -
207D TYR* 2.8 43.1 - - + +
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Residues in contact with GLN 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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544A G 2.4 32.0 + - - +
545A C 2.9 30.5 + - - -
15D GLU* 3.9 2.2 - - - -
58D LEU* 2.7 24.5 + - + +
59D ARG* 2.4 41.8 + - - +
61D LYS* 1.3 113.4 - - - +
63D LYS* 1.3 63.8 + - - +
65D ARG* 3.3 10.1 + - - +
66D ARG* 3.2 42.4 + - - +
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Residues in contact with LYS 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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15D GLU* 3.0 50.4 + - + +
17D VAL* 3.5 28.5 - - + +
19D LEU* 5.2 3.0 - - + +
59D ARG* 2.4 15.9 + - - +
60D GLU* 3.0 41.3 + - - +
61D LYS 2.9 0.4 + - - -
62D GLN* 1.3 77.2 - - - +
64D LEU* 1.3 66.5 + - - +
65D ARG 2.7 0.2 + - - -
66D ARG* 3.0 9.8 + - - +
67D ILE* 3.2 22.1 + - + +
197D PRO* 2.9 33.4 - - + +
198D VAL* 3.8 4.0 - - + -
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Residues in contact with LEU 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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60D GLU 3.0 5.4 + - - +
61D LYS 3.7 5.6 - - - +
63D LYS* 1.3 78.1 - - - +
65D ARG* 1.3 66.5 + - - +
67D ILE* 3.4 22.2 - - + +
68D TYR* 3.6 18.8 + - + -
75D PHE* 3.3 24.9 - - + -
93D PHE* 5.0 2.7 - - + -
94D LEU* 4.0 16.4 - - + -
97D LEU* 3.5 22.2 - - + -
196D LEU* 4.6 2.0 - - + -
198D VAL* 3.1 43.7 - - + +
200D GLU* 6.4 0.2 - - - -
203D VAL* 4.0 13.0 - - + -
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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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545A C 3.5 19.6 + - - -
546A G 3.5 13.3 + - - -
61D LYS* 2.7 25.2 + - - +
62D GLN* 3.3 30.5 + - - +
63D LYS 2.7 3.6 + - - -
64D LEU* 1.3 75.3 - - - +
66D ARG* 1.3 75.1 + - + +
67D ILE 3.1 0.2 + - - -
68D TYR* 3.1 11.8 + - - +
69D GLY* 3.3 6.4 + - - -
70D ILE* 2.9 32.1 + - - +
71D SER* 4.1 0.2 - - - +
72D GLU* 3.3 30.2 + - - +
75D PHE* 3.0 47.1 - - + -
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Residues in contact with ARG 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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543A C 5.4 4.0 + - - -
544A G 2.9 26.9 + - - -
545A C 5.6 0.2 + - - -
4D TYR* 6.4 0.7 - - + -
11D LEU* 3.7 47.1 + - + +
14D ARG* 4.4 10.7 - - - +
15D GLU* 4.2 4.6 + - - -
19D LEU* 5.3 7.2 - - + -
21D LEU* 2.8 26.1 - - + +
59D ARG* 3.4 25.1 - - - +
62D GLN* 3.2 27.9 + - - +
63D LYS* 3.0 5.2 + - - +
65D ARG* 1.3 89.8 - - + +
67D ILE* 1.3 57.3 + - - +
69D GLY* 2.4 29.1 + - - +
70D ILE 5.0 0.7 - - - +
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Residues in contact with ILE 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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19D LEU* 3.6 23.3 - - + +
20D TYR 6.3 1.1 - - - +
21D LEU* 3.1 18.7 + - - +
63D LYS* 3.2 16.4 + - + +
64D LEU* 3.4 28.3 - - - +
65D ARG 3.1 0.2 + - - -
66D ARG* 1.3 78.4 - - - +
68D TYR* 1.3 76.1 + - + +
114D ARG* 2.8 31.4 + - - +
196D LEU* 3.8 19.3 - - + -
197D PRO* 4.0 27.4 - - + -
198D VAL* 4.5 4.0 - - + -
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Residues in contact with TYR 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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21D LEU* 4.2 3.1 - - - -
64D LEU* 3.7 23.1 - - + +
65D ARG 3.1 6.7 + - - +
66D ARG 3.1 0.4 - - - -
67D ILE* 1.3 93.6 - - + +
69D GLY* 1.3 66.5 + - - +
70D ILE* 3.3 22.3 - - + +
94D LEU* 4.5 3.6 - - - +
97D LEU* 3.3 45.0 - - + +
98D GLU* 2.8 33.3 + - - -
100D ARG* 5.3 3.9 + - - -
102D ASP* 4.9 6.4 - - - +
103D ASN* 4.7 12.8 - - + -
107D ARG* 5.5 0.2 + - - -
114D ARG* 4.2 22.8 + - - +
194D LEU* 4.3 1.7 - - - +
196D LEU* 2.9 34.7 - - + +
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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