Contacts of the strand formed by residues 53 - 61 (chain B) in PDB entry 1Y8G
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 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B PRO* 3.5 4.4 - - - +
49B HIS* 3.0 22.3 + - - +
50B ILE* 2.8 40.1 + - + +
51B GLY 3.5 0.8 + - - -
52B ASN* 1.3 80.6 - - + +
54B ARG* 1.3 60.4 + - - +
55B LEU* 3.8 2.4 + - + -
70B ALA* 4.3 12.6 - - + -
71B ARG 3.3 3.4 - - - +
72B HIS* 3.2 41.6 - + + -
73B ILE* 4.5 0.2 - - - -
79B VAL* 3.8 15.3 - - + -
81B VAL* 4.7 4.9 - - + -
117B GLU* 2.8 31.5 + - - +
119B ILE* 4.3 4.3 - - + -
128B VAL* 3.5 41.6 - - + +
356B ALA* 3.5 15.9 - - - +
360B LEU* 4.1 5.3 - - + +
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Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO* 4.1 17.6 - - + +
49B HIS* 3.3 36.3 + - - +
53B TYR* 1.3 72.5 - - - +
55B LEU* 1.3 72.2 + - - +
56B LEU* 3.4 14.2 + - + +
70B ALA* 3.2 2.5 - - - -
71B ARG* 2.8 65.3 + - + +
73B ILE* 4.2 17.6 - - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B HIS* 3.2 42.6 + - + +
50B ILE* 4.3 21.1 - - + -
53B TYR* 4.9 2.2 - - + -
54B ARG* 1.3 80.7 + - - +
56B LEU* 1.3 63.1 + - - +
68B LYS* 3.9 42.4 - - + +
69B LEU 3.8 2.5 - - - +
70B ALA* 4.2 15.3 - - + -
81B VAL* 4.3 18.4 - - + -
83B ILE* 4.0 11.4 - - + -
126B TYR* 6.0 0.7 - - + -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ARG* 3.9 19.5 - - + +
55B LEU* 1.3 81.1 - - - +
57B LYS* 1.3 65.3 + - + +
68B LYS* 5.6 1.7 - - - -
69B LEU* 2.7 31.3 + - + +
70B ALA* 4.1 18.6 - - - +
71B ARG* 3.6 35.4 - - + +
78B GLU* 5.1 7.9 - - + +
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 1.3 80.5 - - + +
58B THR* 1.3 66.2 + - - +
59B ILE* 3.5 17.9 + - + +
68B LYS* 3.3 7.3 - - - +
69B LEU* 2.7 58.4 + - + +
131B TYR* 5.8 2.9 + - - -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 1.3 76.1 - - - +
59B ILE* 1.3 62.0 + - - +
60B GLY 3.3 27.4 - - - +
61B LYS* 4.1 15.0 - - + -
66B LYS* 4.3 15.4 - - + -
67B VAL 3.6 7.2 - - - +
68B LYS* 3.3 22.5 - - + +
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Residues in contact with ILE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 3.5 31.2 + - + +
58B THR* 1.3 76.4 - - - +
60B GLY* 1.3 57.5 + - - +
67B VAL* 2.9 34.7 + - + +
68B LYS 4.4 1.3 - - - +
69B LEU* 4.0 23.1 - - + +
80B ALA* 4.8 2.9 - - + -
131B TYR* 3.6 38.6 - - + +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 3.3 14.8 - - - +
59B ILE* 1.3 81.1 - - - +
61B LYS* 1.3 61.5 + - - -
66B LYS* 3.7 2.1 - - - -
67B VAL* 3.1 37.8 + - - -
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Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 4.1 12.3 - - + -
60B GLY* 1.3 75.9 - - - +
62B GLY* 1.3 73.7 + - - +
65B ALA 4.0 2.9 - - - +
66B LYS* 3.8 30.4 - - + +
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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