Contacts of the strand formed by residues 72 - 82 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6I ASN* 3.6 37.5 - - + +
7I PRO* 3.5 31.3 - - + +
8I LEU* 4.7 4.3 - - + -
47I ASN* 3.6 31.6 - - + +
49I ILE* 4.2 19.3 - - + -
70J GLY 4.2 1.3 - - - +
71J ALA* 1.3 70.5 - - - +
73J VAL* 1.3 59.4 + - - +
74J PRO* 3.6 1.7 - - - +
163J TRP* 3.7 7.6 - - - -
14K LEU* 3.8 8.0 - - + +
15K PRO* 4.1 18.8 - - + -
51K ILE* 4.3 1.1 - - + -
74L PRO* 3.9 31.2 - - + -
162L LEU* 4.6 5.8 - - + -
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Residues in contact with VAL 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ILE* 4.6 3.6 - - + -
46I VAL* 4.0 19.3 - - + -
47I ASN 2.8 13.7 + - - +
48I LEU* 3.6 5.3 - - + -
49I ILE* 2.9 24.7 + - - +
67J LEU* 4.2 14.6 - - + -
71J ALA* 3.9 23.1 - - + +
72J LEU* 1.3 74.5 - - - +
74J PRO* 1.4 66.5 - - - +
75J THR* 2.9 24.3 + - - +
161J ALA* 3.9 16.6 - - + -
162J LEU 3.6 16.8 - - - +
163J TRP* 4.2 11.2 - - + -
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Residues in contact with PRO 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ILE* 5.3 1.3 - - + -
72H LEU* 3.8 31.2 - - + -
7I PRO* 3.8 15.3 - - + -
15I PRO* 4.6 6.3 - - + -
49I ILE* 3.4 14.8 - - + +
51I ILE* 4.0 19.5 - - + -
72J LEU 3.6 8.5 - - - +
73J VAL* 1.4 79.3 - - - +
75J THR* 1.3 60.7 + - - +
162J LEU* 2.9 52.3 + - + +
163J TRP* 4.5 4.7 - - + -
164J TYR* 5.6 1.1 - - + -
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Residues in contact with THR 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ILE* 5.0 1.1 - - + -
48I LEU* 3.4 27.7 - - + +
49I ILE 2.9 11.0 + - - -
50I ARG* 3.2 8.5 - - - +
51I ILE* 2.9 25.8 + - - +
73J VAL* 2.9 23.5 + - - +
74J PRO* 1.3 75.7 + - - +
76J ALA* 1.3 65.0 + - - +
77J TYR* 3.9 14.6 + - + -
159J ALA* 3.6 26.2 - - + -
160J ALA 3.5 15.7 - - - +
161J ALA* 4.1 5.2 - - + +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ARG* 5.3 0.2 - - - -
51I ILE* 3.5 25.3 - - + +
53J PYR 3.9 12.3 - - + +
75J THR* 1.3 71.6 - - - +
77J TYR* 1.3 61.2 + - - +
93J ILE* 3.7 4.6 - - - +
107J ILE* 3.7 29.4 - - + -
109J GLU* 4.6 7.6 - - - +
159J ALA* 3.2 3.1 - - - +
160J ALA* 2.8 34.8 + - + +
7013J AG2 5.8 0.2 - - - +
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Residues in contact with TYR 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PHE* 4.0 13.5 - + - -
48I LEU* 4.0 22.0 - - + -
50I ARG* 2.8 71.4 + - + +
51I ILE 5.4 0.2 + - - -
75J THR* 3.9 14.6 + - + -
76J ALA* 1.3 75.0 - - - +
78J GLY* 1.3 59.5 + - - +
79J TYR* 3.8 21.3 - + - -
93J ILE* 4.1 2.7 - - - +
109J GLU* 3.6 17.5 + - - +
157J PHE* 3.5 22.0 - + + -
158J ALA 3.3 14.1 - - - +
159J ALA* 3.5 5.4 - - + -
7004J MRD 3.7 8.4 - - + +
52K SER* 2.7 35.9 + - - -
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Residues in contact with GLY 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ARG* 4.4 2.9 - - - -
77J TYR* 1.3 74.7 - - - +
79J TYR* 1.3 63.3 + - - +
91J ALA* 3.7 7.8 - - - +
92J ALA 5.2 0.9 - - - -
109J GLU* 3.9 14.4 - - - +
110J TYR 4.6 4.9 - - - -
111J GLU* 3.7 14.6 - - - -
157J PHE* 3.5 2.4 - - - -
158J ALA 2.9 31.3 + - - +
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Residues in contact with TYR 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PHE* 3.9 15.7 - + + -
50I ARG* 3.9 24.7 + - - -
77J TYR* 3.8 17.5 - + - -
78J GLY* 1.3 76.2 - - - +
80J ILE* 1.3 66.4 + - - +
81J ILE* 4.0 29.2 - - + -
91J ALA* 4.4 0.2 - - - -
111J GLU* 3.2 25.2 + - - +
155J CYS* 4.5 0.9 - - - -
156J ALA 3.1 14.4 - - - +
157J PHE* 4.0 14.8 - - + -
7004J MRD 3.2 40.1 + - + +
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Residues in contact with ILE 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J TYR* 1.3 78.8 - - - +
81J ILE* 1.3 73.9 + - - +
82J SER* 5.7 0.2 - - - -
89J ILE* 3.6 33.3 - - + +
90J SER 3.4 24.7 - - - +
111J GLU* 4.0 8.5 - - + -
112J GLY* 3.6 31.6 - - - -
113J LYS* 4.0 13.9 - - + +
155J CYS* 3.2 4.7 - - - -
156J ALA* 3.0 36.3 + - + +
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Residues in contact with ILE 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I PRO* 3.4 38.8 - - + +
34I PHE* 4.5 4.3 - - + -
79J TYR* 4.0 16.7 - - + -
80J ILE* 1.3 85.4 - - - +
82J SER* 1.3 66.7 + - - +
153J LEU* 3.8 23.3 - - + -
154J GLY 3.3 10.8 - - - +
155J CYS* 3.9 14.6 - - + -
7004J MRD 3.5 26.0 - - + +
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Residues in contact with SER 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ILE* 5.4 0.7 - - - -
81J ILE* 1.3 79.2 - - - +
83J ASP* 1.3 62.0 + - - +
84J VAL* 3.2 15.0 + - - +
87J GLU* 2.7 30.3 + - - -
89J ILE* 3.8 13.4 - - - +
113J LYS* 5.9 1.3 - - - -
150J VAL* 3.5 20.6 - - - +
153J LEU* 3.4 2.0 - - - +
154J GLY 2.9 32.5 + - - +
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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