Contacts of the strand formed by residues 100 - 106 (chain B) in PDB entry 1YAA
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 VAL 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B PHE* 3.5 32.8 - - + -
94B ALA* 3.6 37.2 - - + +
95B LEU* 3.8 23.1 - - + -
98B ASP* 3.5 2.9 - - - +
99B ARG* 1.3 78.3 - - - +
101B ILE* 1.3 63.8 + - - +
102B SER* 3.5 23.2 + - - +
269B LEU* 3.3 14.1 - - + +
280B LYS* 3.5 14.2 + - - -
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Residues in contact with ILE 101 (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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100B VAL* 1.3 70.5 - - - +
102B SER* 1.3 61.1 + - - +
103B VAL* 4.4 7.9 - - + -
269B LEU* 2.9 51.2 - - - +
270B LEU* 4.3 15.3 - - + -
280B LYS* 3.6 38.6 - - + +
283B VAL* 3.8 27.1 - - + -
284B THR* 3.4 25.8 - - + +
287B LEU* 3.4 26.2 - - + -
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Residues in contact with SER 102 (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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74B THR* 4.8 3.5 - - - +
80B THR* 4.0 28.7 + - - +
81B SER* 5.8 0.2 - - - -
84B ALA* 3.7 6.9 - - - +
100B VAL* 3.5 17.5 + - - +
101B ILE* 1.3 70.6 - - - +
103B VAL* 1.3 67.1 + - - +
269B PHE* 2.8 36.5 + - - -
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Residues in contact with VAL 103 (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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74B THR* 3.8 26.2 - - + +
80B THR* 4.0 4.0 - - - -
101B ILE* 4.4 5.8 - - + -
102B SER* 1.3 81.0 - - - +
104B GLN* 1.3 59.7 + - - +
114B ILE* 4.4 7.6 - - + -
269B PHE* 2.7 67.9 + - + +
284B THR* 5.3 4.3 - - + -
287B LEU* 4.1 28.0 - - + -
291B ILE* 4.3 21.8 - - + -
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Residues in contact with GLN 104 (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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71B LEU* 3.9 2.4 - - - +
74B THR 3.0 19.6 + - - +
75B GLY* 3.3 3.3 - - - -
76B LEU* 2.8 29.3 + - - +
79B LEU* 3.5 27.3 - - + +
80B THR* 3.6 12.3 - - + +
103B VAL* 1.3 72.7 - - - +
105B SER* 1.3 65.2 + - - +
266B ARG 5.5 1.8 + - - -
267B VAL* 5.5 1.8 - - - +
268B GLY 3.7 8.5 - - - +
269B CYS* 4.4 1.1 - - - +
291B ILE* 4.1 17.8 - - - +
298B PRO* 3.3 34.2 - - + +
299B PRO* 3.2 27.5 + - - +
303B ALA* 3.4 9.7 - - - +
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Residues in contact with SER 105 (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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103B VAL 3.6 0.4 + - - -
104B GLN* 1.3 80.8 + - - +
106B LEU* 1.3 62.3 + - - +
107B SER 2.9 23.0 + - - -
110B GLY 3.9 2.9 - - - -
111B ALA* 3.4 32.2 - - - +
114B ILE* 3.9 15.5 - - - -
266B ARG 3.5 4.3 - - - +
267B VAL* 4.5 0.3 - - - -
268B GLY 2.9 25.3 + - - +
269B PHE 3.7 6.5 + - - -
298B PRO* 4.9 5.5 - - - +
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Residues in contact with LEU 106 (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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106A LEU* 3.4 48.9 - - + -
295A VAL* 4.1 21.4 - - + +
297A ASN 5.1 0.4 - - - +
299A PRO* 4.3 1.6 - - + -
105B SER* 1.3 71.6 - - - +
107B SER* 1.3 66.9 + - - +
110B GLY* 2.9 26.0 + - - -
266B ARG* 3.5 41.9 + - + +
295B VAL* 3.7 25.6 - - + -
298B PRO* 4.9 3.4 - - + -
299B PRO* 4.0 17.0 - - + -
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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