Contacts of the strand formed by residues 49 - 58 (chain D) in PDB entry 1I3R
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 ARG 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B ASP* 5.8 0.2 + - - -
69B ASP* 3.2 48.0 + - - +
70B VAL* 4.4 0.2 - - - +
44D TYR* 2.8 82.9 + - + +
46D GLY 4.0 0.3 - - - +
48D GLN* 1.3 82.7 - - + +
50D VAL* 1.3 69.1 + - - +
51D ARG* 4.6 9.7 - - - +
69D ASP* 3.7 23.0 + - - -
106D ARG* 4.4 1.1 - - - +
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Residues in contact with VAL 50 (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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42D HIS 3.4 9.9 - - - +
43D PHE* 3.2 40.2 - - + -
44D TYR* 5.3 0.4 - - - -
46D GLY 4.1 5.4 - - - +
47D THR* 4.1 14.1 - - - +
49D ARG* 1.3 85.5 + - - +
51D ARG* 1.3 70.6 + - - +
68D SER* 4.3 2.1 + - - -
69D ASP* 4.3 5.9 - - - +
101D VAL* 3.7 30.9 - - + +
105D CYS* 3.9 12.6 - - + -
106D ARG* 4.0 19.4 + - + +
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Residues in contact with ARG 51 (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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51B ARG* 3.6 37.2 - - - +
65B ARG* 6.0 1.2 - - - +
67B ASP* 4.4 4.2 + - - -
69B ASP* 5.0 5.5 + - - -
40D GLU 3.4 2.1 - - - +
41D CYS* 3.5 1.2 - - - -
42D HIS* 2.8 62.8 + - + +
44D TYR* 4.9 10.9 + - + -
49D ARG* 4.6 9.4 - - - +
50D VAL* 1.3 77.8 - - - +
52D LEU* 1.3 65.1 + - - +
53D LEU* 3.7 29.8 - - - +
65D ARG* 4.8 5.7 - - - +
67D ASP* 2.7 43.1 + - - +
68D SER* 3.4 5.6 - - - +
69D ASP* 3.7 20.7 + - - +
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Residues in contact with LEU 52 (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 PHE* 3.3 42.8 - - + -
40D GLU 3.4 17.5 - - - +
50D VAL 4.3 0.2 - - - -
51D ARG* 1.3 74.5 - - - +
53D LEU* 1.3 62.1 + - - +
54D VAL* 4.2 19.7 - - + -
66D PHE* 3.3 12.9 - - + +
67D ASP* 3.5 3.8 - - - +
68D SER* 2.6 47.6 + - - +
97D LYS* 4.1 10.3 - - - +
100D GLU* 4.0 20.6 - - + +
101D VAL* 4.1 17.2 - - + +
105D CYS* 3.8 11.2 - - - -
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Residues in contact with LEU 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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40D GLU* 2.8 60.7 + - - +
42D HIS* 4.3 10.1 - - + +
51D ARG* 3.7 28.2 + - - +
52D LEU* 1.3 74.6 - - - +
54D VAL* 1.3 65.3 + - - +
55D ARG* 4.0 16.3 + - + -
65D ARG* 4.0 39.9 - - + +
66D PHE 3.3 11.0 - - - +
67D ASP* 4.1 14.1 - - + -
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Residues in contact with VAL 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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8D PHE* 5.2 1.3 - - + -
10D GLU* 4.6 1.6 - - - +
37D CYS* 3.9 8.1 - - - -
38D LYS 3.3 4.9 - - - +
39D SER* 3.7 30.5 - - - +
52D LEU* 4.2 17.9 - - + -
53D LEU* 1.3 75.5 - - - +
55D ARG* 1.3 63.9 + - - +
56D TYR* 3.5 32.5 - - + +
65D ARG* 3.1 9.8 - - - +
66D PHE* 2.9 41.9 + - + +
97D LYS* 4.3 20.9 - - - +
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Residues in contact with ARG 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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141C ASP* 2.9 31.5 + - - +
142C ASP* 4.2 4.6 - - - +
37D CYS* 3.5 4.9 - - - -
38D LYS* 2.7 43.1 + - + +
40D GLU* 3.0 41.3 + - - -
53D LEU* 4.1 19.5 - - + +
54D VAL* 1.3 79.0 - - - +
56D TYR* 1.3 63.5 + - - +
57D PHE* 3.6 30.8 - - + -
62D GLU* 3.5 32.5 + - - +
64D LEU 3.7 3.6 - - - -
65D ARG* 4.2 8.5 - - + +
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Residues in contact with TYR 56 (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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69C ASN* 5.9 1.1 - - - -
10D GLU* 2.8 35.4 + - + +
11D GLY 4.8 2.1 + - - -
13D LYS* 4.6 11.9 - - - +
35D GLU* 4.6 13.7 - - - -
36D TYR 3.7 2.2 - - - -
37D CYS* 3.6 17.5 - - + -
54D VAL* 3.5 23.9 - - + +
55D ARG* 1.3 76.0 - - - +
57D PHE* 1.3 62.8 + - - +
62D GLU* 3.3 5.4 - - - +
63D ASN* 3.0 39.9 + - - +
64D LEU* 2.9 43.4 + - + +
65D ARG* 4.5 0.9 - - - -
73D PHE* 3.9 18.8 - + - -
87D TRP* 3.7 25.5 - + - -
93D PHE* 5.9 0.3 - - - -
97D LYS* 4.8 4.3 - - - -
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Residues in contact with PHE 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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142C ASP 3.9 5.4 - - - -
143C HIS* 3.6 31.4 - - + -
13D LYS* 6.3 0.4 - - - -
34D LEU 3.6 0.9 - - - +
35D GLU* 3.9 6.3 - - - +
36D TYR* 2.8 67.8 + + + +
38D LYS* 3.5 30.5 - - + -
55D ARG* 3.6 46.4 - - + -
56D TYR* 1.3 76.0 - - - +
58D TYR* 1.3 60.0 + - - +
59D ASN 4.0 9.0 - - - +
61D GLU 3.1 6.3 - - - +
62D GLU* 3.6 33.2 - - + -
63D ASN* 4.2 1.8 - - - -
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Residues in contact with TYR 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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70C LEU* 4.0 15.3 - - + -
73C MET* 3.7 36.6 - - + -
74C LYS* 3.9 6.5 - - - -
77C SER* 3.2 32.5 + - - -
80C THR 4.1 4.0 + - - -
82C ASP* 4.6 0.7 - - - +
33D PHE* 3.3 25.2 - - + -
34D LEU 3.4 13.0 - - - -
35D GLU* 4.4 2.7 - - - +
57D PHE* 1.3 73.4 - - - +
59D ASN* 1.3 97.3 + - + +
60D LEU 3.1 0.7 + - - -
61D GLU* 2.9 22.6 + - - +
63D ASN* 3.5 19.3 - - - +
79D LEU* 3.8 21.3 - - + -
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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