Contacts of the strand formed by residues 54 - 60 (chain C) in PDB entry 2Y1T
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 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PRO* 4.4 12.6 - - + +
1C MET* 3.2 30.4 - - + +
50C LEU* 4.2 4.1 - - + +
51C PRO* 2.9 33.7 + - + +
52C GLU 3.4 15.5 - - - -
53C GLY* 1.4 78.2 - - - +
55C GLU* 1.3 62.1 + - - +
81C GLU* 3.2 27.5 + - - +
113C ILE* 3.7 25.6 - - + -
114C MET* 3.4 20.6 - - - -
115C LYS* 3.5 33.9 - - + +
116C LYS* 3.7 4.6 - - - +
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Residues in contact with GLU 55 (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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21B GLY 4.6 2.6 - - - +
22B ASP* 5.7 0.5 - - - -
23B TRP* 2.8 36.5 + - - -
112B ARG* 3.1 22.8 + - - +
50C LEU* 3.8 4.9 - - - -
54C TYR* 1.3 74.6 - - - +
56C ALA* 1.3 58.8 + - - +
57C HIS* 2.7 31.5 + - + +
78C VAL* 4.2 5.5 - - + +
79C ILE 3.3 16.8 - - - +
80C ASP* 4.4 7.2 - - - +
113C ILE* 3.1 6.1 - - - +
114C MET 2.9 39.8 + - - +
116C LYS* 3.6 20.3 - - + +
117C MET 5.0 0.2 + - - -
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Residues in contact with ALA 56 (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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50C LEU* 3.5 11.5 - - + +
55C GLU* 1.3 71.4 - - - +
57C HIS* 1.3 67.1 + - - +
77C GLY 3.5 0.3 - - - +
78C VAL* 3.2 7.1 - - - +
79C ILE* 2.8 47.0 + - + +
90C TRP* 3.5 32.1 - - + -
111C PHE* 4.0 7.9 - - + -
112C ARG 3.3 10.8 - - - +
113C ILE* 4.3 0.4 - - + +
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Residues in contact with HIS 57 (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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57A HIS* 6.2 1.4 - - - -
23B TRP* 4.2 4.9 - + - -
112B ARG* 5.0 0.7 - - - -
114B MET* 5.0 5.2 - - + -
23C TRP* 3.4 16.6 - - + -
55C GLU* 2.7 36.0 + - + +
56C ALA* 1.3 82.1 - - - +
58C VAL* 1.3 61.0 + - - +
76C MET* 3.6 42.2 - - + +
77C GLY 3.2 3.6 - - - -
78C VAL* 4.4 6.7 - - + -
111C PHE* 3.1 25.3 - - - +
112C ARG* 2.9 17.3 + - + +
114C MET* 3.5 40.0 - - + +
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Residues in contact with VAL 58 (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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26C LEU* 5.1 0.7 - - + -
44C LEU* 5.1 4.7 - - + -
57C HIS* 1.3 77.4 - - - +
59C VAL* 1.3 63.2 + - - +
72C GLN* 3.1 14.1 + - - +
76C MET* 3.2 6.2 - - - -
77C GLY* 2.8 43.0 + - - +
79C ILE* 4.1 19.3 - - + -
90C TRP* 3.9 31.4 - - + -
91C PHE 5.3 2.7 - - - +
92C PHE* 4.8 2.9 - - + -
109C CYS* 3.6 32.5 - - + -
110C GLN 3.4 7.0 - - - +
111C PHE* 4.1 4.0 - - + -
143C DUD 4.8 5.8 - - + +
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Residues in contact with VAL 59 (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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74A ASN 4.4 0.9 - - - +
76A MET* 4.2 31.0 - - + +
78A VAL* 4.6 3.4 - - + -
23C TRP* 3.5 28.9 - - + -
58C VAL* 1.3 77.1 - - - +
60C PRO* 1.3 80.9 - - + +
72C GLN* 3.4 6.3 - - - -
75C SER 4.3 4.3 - - - +
76C MET* 3.8 27.6 - - + -
109C CYS* 3.2 3.7 - - - +
110C GLN* 2.9 41.6 + - + +
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Residues in contact with PRO 60 (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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73A THR 4.3 6.5 - - - +
74A ASN* 3.3 38.8 - - - +
75A SER* 3.7 10.3 - - - +
76A MET 5.1 0.7 - - - +
59C VAL* 1.3 100.3 - - + +
61C ARG* 1.3 71.7 + - - +
62C SER 3.9 0.2 + - - -
64C THR* 4.0 15.0 - - + -
65C TYR 5.9 0.4 - - - +
70C VAL 5.8 1.3 - - - +
71C ILE* 5.4 0.4 - - - -
72C GLN* 3.1 30.4 - - + +
92C PHE* 4.2 5.6 - - + -
108C ILE 4.1 8.5 - - - +
109C CYS* 4.2 2.2 - - + -
110C GLN* 3.8 3.3 - - - +
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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