Contacts of the strand formed by residues 104 - 108 (chain T) in PDB entry 1Y5A
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 MET 104 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T LEU* 4.7 0.9 - - + -
53T VAL* 3.5 6.2 - - - +
54T SER* 2.9 37.0 + - - +
55T ALA 3.4 20.9 - - - +
56T ALA* 3.8 10.5 - - - +
58T CYS* 3.8 9.6 - - + +
59T TYR* 3.6 47.3 - - - +
63T ILE* 4.6 3.8 - - + -
88T SER* 4.4 7.6 - - - -
89T ILE 3.3 17.5 - - - +
90T VAL* 4.0 7.9 - - + -
103T ILE* 1.3 77.3 - - - +
105T LEU* 1.3 76.4 + - - +
106T ILE* 3.9 22.7 - - + -
237T TRP* 4.6 2.0 - - - -
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Residues in contact with LEU 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE* 4.2 6.7 - - + -
51T TRP* 3.8 15.9 - - + -
52T VAL 3.5 6.5 - - - +
53T VAL* 3.5 30.5 - - + -
87T LYS 4.2 0.2 - - - +
88T SER* 3.4 3.5 - - - -
89T ILE* 2.8 38.0 + - + +
103T ILE* 6.1 0.2 - - + -
104T MET* 1.3 74.3 - - - +
106T ILE* 1.3 65.7 + - - +
107T LYS 4.3 0.2 - - - -
237T TRP* 3.8 23.8 - - + -
238T ILE* 4.2 20.0 - - + -
241T THR* 3.8 32.5 - - + -
242T ILE* 4.1 16.4 - - + -
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Residues in contact with ILE 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T LEU* 3.8 37.0 - - + -
51T TRP* 3.4 7.1 - - - -
52T VAL* 2.9 43.4 + - + +
54T SER* 4.5 6.7 - - - -
63T ILE* 3.9 11.2 - - + -
65T VAL* 4.1 16.2 - - + -
85T ALA* 3.6 29.2 - - + -
87T LYS 3.5 4.7 - - - +
88T SER* 3.9 11.0 - - - +
104T MET* 3.9 21.5 - - + +
105T LEU* 1.3 79.9 - - - +
107T LYS* 1.3 64.3 + - - +
108T LEU* 4.0 0.4 + - + -
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Residues in contact with LYS 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T IMD 3.0 30.4 - - - -
50T GLN* 3.4 30.1 - - + +
51T TRP* 3.5 29.2 - - + +
85T ALA* 3.3 7.4 - - - -
86T SER* 2.8 32.2 + - - +
87T LYS* 2.9 37.1 + - + -
106T ILE* 1.3 74.3 - - - +
108T LEU* 1.3 66.8 + - - +
245T ASN* 2.7 37.4 + - - +
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Residues in contact with LEU 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T LEU* 4.3 11.9 - - + -
49T SER 3.5 24.0 - - - +
50T GLN* 2.9 25.1 + - - +
51T TRP 4.6 0.2 - - - +
52T VAL* 4.4 7.6 - - + -
65T VAL* 3.5 41.7 - - + -
67T LEU* 4.8 3.4 - - + -
83T ILE* 3.9 17.7 - - + +
84T SER 3.9 3.6 - - - +
86T SER* 3.9 1.5 + - - -
106T ILE 5.1 0.9 - - - +
107T LYS* 1.3 87.1 - - - +
109T LYS* 1.3 65.2 + - - +
110T SER* 3.2 21.2 + - - +
112T ALA* 4.1 15.7 - - + +
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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