Contacts of the strand formed by residues 36 - 42 (chain C) in PDB entry 6PI7
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 TYR 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ASP* 5.5 0.3 + - - -
35C TYR* 1.3 70.6 - - - +
37C ILE* 1.3 60.7 + - - +
38C HIS* 3.4 15.7 - + - +
53C SER* 4.9 7.2 - - - -
54C ILE 3.3 9.6 - - - -
55C TYR* 3.6 29.9 - + + +
60C SER* 5.2 5.0 + - - -
101C ARG* 3.5 6.6 - - - +
102C SER* 3.1 44.9 + - - +
103C HIS 3.3 20.9 - - - -
104C TYR* 3.5 41.8 + + - -
106C PRO* 5.2 1.6 - - + -
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Residues in contact with ILE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.3 10.3 - - + -
25C CYS* 5.6 0.7 - - - -
27C ALA* 5.5 0.4 - - + -
30C PHE* 4.1 30.1 - - + -
32C VAL* 4.5 20.9 - - + +
35C TYR* 4.3 7.6 - - + +
36C TYR* 1.3 79.0 - - - +
38C HIS* 1.3 65.3 + - - +
39C TRP* 5.1 3.8 - - - +
53C SER* 3.3 4.0 - - - -
54C ILE* 2.9 43.8 + - + +
56C PRO* 5.5 1.3 - - + -
73C ILE* 3.9 3.8 - - + +
82C ALA* 3.6 28.0 - - + -
99C CYS* 3.8 19.1 - - - -
100C ALA 3.4 7.9 - - - +
101C ARG* 4.4 3.6 - - + -
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Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.8 23.0 - - + +
36C TYR* 3.4 17.2 - + + +
37C ILE* 1.3 78.6 - - - +
39C TRP* 1.3 69.6 + - - +
40C VAL* 4.0 8.7 - - + -
50C TRP* 3.6 15.1 + + + -
52C ALA 3.3 5.8 - - - +
53C SER* 3.6 24.7 - - - -
99C CYS* 3.2 9.0 - - - -
100C ALA* 2.8 46.7 + - + +
101C ARG 4.4 0.4 - - - -
102C SER* 2.7 35.4 + - - -
114C LEU* 4.4 10.3 - - + +
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Residues in contact with TRP 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 3.9 20.6 - - + -
23C LEU* 3.7 31.6 - - + -
24C SER 3.7 25.6 - - - -
25C CYS* 3.8 22.9 - - + -
37C ILE* 5.1 1.9 - - + +
38C HIS* 1.3 75.5 - - - +
40C VAL* 1.3 59.1 + - - +
50C TRP* 4.0 1.0 - - - -
51C VAL* 2.9 44.9 + - + +
52C ALA 2.9 12.1 + - - +
73C ILE* 3.5 26.9 - - + +
82C ALA* 4.2 7.7 - - - +
83C TYR 3.7 12.5 + - - +
84C LEU* 3.6 37.1 - - + +
97C TYR* 4.2 14.8 - - + -
98C TYR 3.3 25.4 - - - -
99C CYS* 4.0 5.8 - - + -
121C THR* 4.9 0.4 - - + -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.0 17.5 - - + -
38C HIS* 4.0 10.9 - - + -
39C TRP* 1.3 80.1 - - - +
41C ARG* 1.3 59.6 + - - +
48C LEU* 4.0 17.0 - - + -
49C GLU 3.5 25.8 - - - +
50C TRP* 4.2 13.2 - - + -
51C VAL* 4.3 0.4 - - - -
97C TYR* 3.7 1.0 - - - -
98C TYR* 2.7 38.5 + - + +
100C ALA* 5.1 3.6 - - + -
114C LEU* 5.5 3.6 - - + -
117C TRP* 3.8 35.0 - - + -
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 1.3 75.1 - - - +
42C GLN* 1.3 63.1 + - - +
43C ALA 5.4 0.4 - - - +
48C LEU* 3.6 2.4 - - - -
49C GLU* 2.8 73.4 + - - +
51C VAL* 3.5 17.4 - - + +
66C SER* 3.9 14.5 + - - -
67C VAL* 4.0 7.8 - - - +
71C PHE* 3.6 14.1 - - - -
92C GLU* 4.4 9.9 + - - +
93C ASP* 3.0 33.7 + - - +
95C ALA* 4.1 9.6 - - + -
96C VAL 3.1 12.1 - - - +
97C TYR* 2.7 51.6 + - + -
98C TYR* 5.0 1.8 - - - -
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Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 2.9 42.8 + - - -
88B TYR* 3.6 11.1 + - - -
41C ARG* 1.3 77.5 - - - +
43C ALA* 1.3 64.1 + - - +
44C PRO* 3.8 0.7 - - + +
45C GLY 5.9 0.4 - - - +
46C LYS 3.0 28.4 + - - +
47C GLY 3.6 12.8 - - - +
48C LEU* 3.9 9.9 - - + +
49C GLU* 5.8 0.2 - - - -
95C ALA* 3.4 3.3 - - - -
96C VAL* 2.9 38.2 + - + +
98C TYR* 3.8 13.6 + - + -
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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