Contacts of the strand formed by residues 72 - 82 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASN* 3.6 32.5 - - + +
49G ILE* 4.1 19.7 - - + +
70H GLY 4.0 2.7 - - - +
71H ALA* 1.3 68.9 - - - +
73H VAL* 1.3 60.0 + - - +
74H PRO* 3.4 11.1 - - - +
163H TRP* 3.4 13.2 - - - -
7I PRO* 3.5 44.6 - - + +
8I LEU* 5.7 4.4 - - + +
11I TYR* 5.2 7.2 + - - +
13I LYS 5.6 1.3 - - - +
14I LEU* 5.0 3.3 - - + +
15I PRO* 4.1 23.3 - - + -
51I ILE* 4.4 0.7 - - + -
74J PRO* 3.8 27.1 - - + -
162J LEU* 4.6 2.2 - - + -
164J TYR* 4.6 0.4 - - - +
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Residues in contact with VAL 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ILE* 6.4 0.2 - - + -
46G VAL* 4.0 19.1 - - + -
47G ASN 2.8 12.2 + - - +
48G LEU* 3.6 2.0 - - + -
49G ILE* 2.9 21.4 + - - -
67H LEU* 4.0 18.6 - - + -
71H ALA* 3.7 25.4 - - + +
72H LEU* 1.3 74.5 - - - +
74H PRO* 1.3 61.4 - - - +
75H THR* 2.8 27.9 + - - +
161H ALA* 4.0 16.2 - - + -
162H LEU 3.5 20.4 - - - +
163H TRP* 4.0 11.0 - - + -
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Residues in contact with PRO 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 4.9 3.1 - - + -
49G ILE* 3.3 17.0 - - + +
51G ILE* 4.0 17.3 - - + -
72H LEU 3.4 10.3 - - - +
73H VAL* 1.3 78.8 - - - +
75H THR* 1.3 60.4 + - - +
162H LEU* 2.8 58.0 + - + +
163H TRP* 4.4 5.4 - - + -
164H TYR* 5.1 4.5 - - + +
8I LEU* 5.3 6.7 - - + +
49K ILE* 5.1 2.0 - - + -
72L LEU* 3.8 31.6 - - + -
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ILE* 4.7 1.3 - - + -
48G LEU* 3.4 26.9 - - + +
49G ILE 2.8 11.0 + - - -
50G ARG* 3.2 9.4 - - - +
51G ILE* 2.9 24.4 + - - +
73H VAL* 2.8 23.4 + - - +
74H PRO* 1.3 74.7 + - - +
76H ALA* 1.3 72.9 + - - +
77H TYR* 3.8 13.1 - - + -
159H ALA* 3.6 20.2 - - + -
160H ALA 3.4 15.0 - - - +
161H ALA* 4.2 5.2 - - + +
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G ILE* 3.4 26.7 - - + +
53H PYR 3.9 11.2 - - + -
75H THR* 1.3 70.3 - - - +
77H TYR* 1.3 63.9 + - - +
93H ILE* 3.8 3.7 - - - +
107H ILE* 3.8 28.3 - - + -
109H GLU* 4.2 10.1 - - - +
159H ALA* 3.2 1.6 - - - +
160H ALA* 2.8 34.5 + - + +
7012H AG2 4.7 0.2 - - - +
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Residues in contact with TYR 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G PHE* 4.0 13.0 - + - -
48G LEU* 4.0 21.8 - - + -
50G ARG* 2.8 70.7 + - + +
51G ILE 5.1 0.2 + - - -
75H THR* 3.8 14.4 - - + -
76H ALA* 1.3 75.5 - - - +
78H GLY* 1.3 60.1 + - - +
79H TYR* 3.8 22.4 - + - -
93H ILE* 4.6 0.2 - - - -
109H GLU* 3.6 19.9 + - - +
157H PHE* 3.6 15.7 - + + -
158H ALA 3.3 12.3 - - - +
159H ALA* 3.5 10.8 - - + -
7003H MRD 3.4 10.0 - - - +
52I SER* 2.7 35.6 + - - -
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Residues in contact with GLY 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ARG* 4.3 4.3 - - - -
77H TYR* 1.3 75.6 - - - +
79H TYR* 1.3 63.9 + - - +
91H ALA* 3.8 7.7 - - - +
92H ALA 5.5 0.7 - - - -
109H GLU* 3.9 12.8 - - - +
110H TYR 5.0 2.7 - - - -
111H GLU* 3.5 18.2 - - - -
157H PHE* 3.5 1.9 - - - -
158H ALA* 2.9 32.4 + - - +
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Residues in contact with TYR 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G PHE* 3.8 25.4 - + + -
50G ARG* 4.0 21.3 + - - +
77H TYR* 3.8 17.7 - + - -
78H GLY* 1.3 75.2 - - - +
80H ILE* 1.3 65.0 + - - +
81H ILE* 4.0 29.4 - - + -
91H ALA* 4.6 0.4 - - - -
111H GLU* 3.3 22.3 + - - +
155H CYS* 4.4 0.9 - - - -
156H ALA 3.1 13.9 - - - +
157H PHE* 4.1 6.3 - - + -
7003H MRD 3.1 45.5 + - + +
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Residues in contact with ILE 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H TYR* 1.3 79.3 - - - +
81H ILE* 1.3 72.9 + - - +
82H SER* 5.4 0.4 - - - -
89H ILE* 3.5 33.0 - - + +
90H SER 3.4 23.8 - - - +
111H GLU* 3.9 8.3 - - + -
112H GLY* 3.5 33.7 - - - +
113H LYS* 4.0 14.8 - - + +
155H CYS* 3.2 4.5 - - - -
156H ALA* 2.9 38.0 + - + +
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Residues in contact with ILE 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G PRO* 3.5 37.5 - - + +
34G PHE* 4.5 4.0 - - + -
79H TYR* 4.0 15.8 - - + -
80H ILE* 1.3 86.0 - - - +
82H SER* 1.3 66.8 + - - +
89H ILE* 4.5 0.2 - - - -
113H LYS* 6.0 0.9 - - - -
153H LEU* 3.8 23.6 - - + -
154H GLY 3.3 10.5 - - - +
155H CYS* 3.8 15.7 - - + -
7003H MRD 3.8 24.5 - - + +
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Residues in contact with SER 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H ILE* 5.4 0.2 - - - -
81H ILE* 1.3 80.2 - - - +
83H ASP* 1.3 61.6 + - - +
84H VAL* 3.2 15.4 + - - +
87H GLU* 2.7 27.5 + - - -
89H ILE* 3.9 13.0 - - - +
113H LYS* 5.0 5.0 + - - -
150H VAL* 3.4 19.6 - - - +
153H LEU* 3.4 2.5 - - - +
154H GLY 3.0 32.1 + - - +
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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