Contacts of the strand formed by residues 72 - 82 (chain D) in PDB entry 1N13
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 LEU 72 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 5.2 0.8 - - + +
15A PRO* 4.1 18.4 - - + -
51A ILE* 4.7 0.2 - - + -
74B PRO* 3.8 35.0 - - + -
162B LEU* 4.7 1.1 - - + -
164B TYR* 3.7 15.7 - - - +
47C ASN* 3.7 30.5 - - + +
49C ILE* 4.1 18.9 - - + +
70D GLY 4.1 2.7 - - - +
71D ALA* 1.3 69.3 - - - +
73D VAL* 1.3 60.3 + - - +
74D PRO* 3.4 12.5 - - - +
163D TRP* 3.7 12.2 - - - -
8E LEU* 3.5 33.1 - - + +
9E HIS* 4.0 15.7 + - + +
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Residues in contact with VAL 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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43C ILE* 6.2 0.4 - - + -
46C VAL* 3.9 20.0 - - + -
47C ASN 2.8 14.2 + - - +
48C LEU* 5.2 0.9 - - + -
49C ILE* 2.9 24.7 + - - -
67D LEU* 4.3 13.2 - - + -
71D ALA* 3.8 25.1 - - + +
72D LEU* 1.3 72.6 - - - +
74D PRO* 1.3 64.5 - - - +
75D THR* 2.9 24.8 + - - +
161D ALA* 3.8 17.9 - - + -
162D LEU 3.5 17.7 - - - +
163D TRP* 4.1 12.6 - - + -
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Residues in contact with PRO 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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15C PRO* 4.5 7.6 - - + -
49C ILE* 3.4 12.8 - - + +
51C ILE* 3.9 20.2 - - + -
72D LEU 3.4 8.3 - - - +
73D VAL* 1.3 79.6 - - - +
75D THR* 1.3 60.2 + - - +
162D LEU* 2.9 56.5 + - + +
163D TRP* 4.4 5.6 - - + -
6E ASN* 4.7 4.5 - - - +
8E LEU* 4.2 19.5 - - + -
72F LEU* 4.1 24.9 - - + -
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Residues in contact with THR 75 (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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43C ILE* 4.7 1.3 - - + -
48C LEU* 3.5 27.0 - - + +
49C ILE 2.8 10.6 + - - -
50C ARG* 3.2 9.2 - - - +
51C ILE* 3.0 23.5 + - - +
73D VAL* 2.9 23.8 + - - +
74D PRO* 1.3 74.1 + - - +
76D ALA* 1.3 66.1 + - - +
77D TYR* 3.9 15.4 - - + -
159D ALA* 3.6 27.6 - - + -
160D ALA 3.4 14.4 - - - +
161D ALA* 4.2 4.6 - - + +
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Residues in contact with ALA 76 (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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51C ILE* 3.5 25.6 - - + +
53D PYR 3.9 12.6 - - + +
75D THR* 1.3 70.5 - - - +
77D TYR* 1.3 62.4 + - - +
93D ILE* 3.7 3.7 - - - +
107D ILE* 3.9 28.3 - - + -
109D GLU* 4.2 9.4 - - - +
159D ALA* 3.2 2.8 - - - +
160D ALA* 2.8 35.3 + - + +
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Residues in contact with TYR 77 (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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52A SER* 2.7 36.5 + - - -
34C PHE* 4.0 13.0 - + - -
48C LEU* 4.0 15.3 - - + -
50C ARG* 2.8 74.5 + - + +
51C ILE 5.3 0.2 + - - -
75D THR* 3.9 20.2 - - + -
76D ALA* 1.3 75.6 - - - +
78D GLY* 1.3 56.3 + - - +
79D TYR* 3.8 23.1 - + - -
93D ILE* 4.7 0.2 - - - -
109D GLU* 3.5 18.6 + - - +
157D PHE* 3.6 16.8 - + + -
158D ALA 3.3 12.6 - - - +
159D ALA* 3.5 11.0 - - + +
7001D MRD 3.6 8.3 - - - +
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Residues in contact with GLY 78 (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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50C ARG* 4.5 2.7 - - - -
77D TYR* 1.3 75.3 - - - +
79D TYR* 1.3 62.2 + - - +
91D ALA* 3.8 6.5 - - - +
92D ALA 5.3 0.7 - - - -
109D GLU* 3.9 12.6 - - - +
110D TYR 4.7 3.4 - - - -
111D GLU* 3.2 18.4 - - - -
157D PHE* 3.5 2.8 - - - -
158D ALA 2.9 32.8 + - - +
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Residues in contact with TYR 79 (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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34C PHE* 3.8 25.1 - + + -
50C ARG* 4.0 22.9 - - - +
77D TYR* 3.8 21.5 - + - -
78D GLY* 1.3 74.2 - - - +
80D ILE* 1.3 64.9 + - - +
81D ILE* 4.0 28.9 - - + -
91D ALA* 4.5 0.2 - - - -
111D GLU* 3.2 24.9 + - - +
155D CYS* 4.4 2.0 - - - -
156D ALA 3.1 13.5 - - - +
157D PHE* 4.1 6.1 - - + -
7001D MRD 3.4 34.5 + - + +
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Residues in contact with ILE 80 (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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79D TYR* 1.3 79.4 - - - +
81D ILE* 1.3 73.2 + - - +
82D SER* 5.6 0.4 - - - -
89D ILE* 3.6 26.3 - - + +
90D SER 3.5 22.0 - - - +
111D GLU* 4.0 8.1 - - + -
112D GLY* 3.5 33.7 - - - +
113D LYS* 3.9 13.9 - - + +
155D CYS* 3.2 4.5 - - - -
156D ALA* 3.0 44.3 + - + +
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Residues in contact with ILE 81 (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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30C PRO* 3.7 36.6 - - + +
34C PHE* 4.6 3.6 - - + -
79D TYR* 4.0 17.2 - - + -
80D ILE* 1.3 86.1 - - - +
82D SER* 1.3 67.5 + - - +
153D LEU* 3.7 24.7 - - + -
154D GLY 3.2 11.4 - - - +
155D CYS* 3.9 15.0 - - + -
7001D MRD 3.7 24.2 - - + +
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Residues in contact with SER 82 (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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80D ILE* 5.4 0.9 - - - -
81D ILE* 1.3 79.3 - - - +
83D ASP* 1.3 60.9 + - - +
84D VAL* 3.2 15.3 + - - +
87D GLU* 2.7 30.2 + - - -
89D ILE* 3.8 11.6 - - - +
113D LYS* 5.8 1.3 - - - -
150D VAL* 3.4 21.1 - - - +
153D LEU* 3.4 2.1 - - - +
154D GLY 2.9 31.9 + - - -
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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