Contacts of the strand formed by residues 2 - 7 (chain F) 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 GLN 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D VAL* 3.9 2.7 - - - -
121D ASP* 3.2 22.9 + - + +
123D ILE* 3.6 23.3 - - + +
1F MET* 1.3 78.8 - - - +
3F ILE* 1.3 65.0 + - - +
4F LYS* 4.5 21.0 - - + +
49F GLU 4.3 1.2 - - - +
51F PRO* 3.5 22.3 - - - +
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Residues in contact with ILE 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D MET* 6.0 0.7 - - - -
120D VAL* 3.7 17.7 - - + +
121D ASP 2.9 5.6 + - - +
122D LEU* 3.5 28.5 - - + +
123D ILE* 2.8 32.4 + - - +
2F GLN* 1.3 73.8 - - - +
4F LYS* 1.3 72.0 + - - +
5F ILE 3.9 0.2 + - - -
24F ILE* 5.4 2.0 - - + -
48F MET* 3.8 23.6 - - + -
49F GLU 3.6 10.5 - - - +
50F LEU* 4.2 7.0 - - + -
51F PRO* 3.7 18.2 - - + -
111F PHE* 4.2 14.1 - - + -
113F ILE* 4.1 25.1 - - + -
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Residues in contact with LYS 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ILE* 3.2 13.2 - - + +
125D VAL* 4.0 29.6 - - + -
128D LEU* 4.6 6.5 - - + +
2F GLN* 4.5 19.5 + - + +
3F ILE* 1.3 74.8 - - - +
5F ILE* 1.3 59.4 + - - +
48F MET* 3.1 7.4 - - - +
49F GLU* 2.9 74.5 + - + +
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Residues in contact with ILE 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 3.2 31.2 - - + -
123D ILE 2.9 17.0 + - - +
124D GLU* 3.3 13.4 - - + +
125D VAL* 2.9 25.6 + - - +
4F LYS* 1.3 75.6 - - - +
6F LYS* 1.3 61.2 + - - +
7F TYR* 3.7 26.4 + - + +
15F ILE* 3.7 21.3 - - + -
46F VAL* 3.5 32.8 - - + -
47F ALA 3.4 8.7 - - - +
48F MET* 3.9 14.4 - - + -
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Residues in contact with LYS 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL 3.7 9.4 - - - +
126D ASP* 3.9 21.3 - - - +
127D ARG* 4.2 5.2 - - - +
128D LEU* 3.2 25.0 - - + +
5F ILE* 1.3 73.9 - - - +
7F TYR* 1.3 72.9 + - - +
8F LEU 5.8 0.7 - - - -
46F VAL* 3.5 3.3 - - - +
47F ALA* 2.7 42.0 + - + +
86F ASP* 2.8 60.6 + - - +
89F PHE* 3.9 19.9 - - + -
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Residues in contact with TYR 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D LEU* 5.3 0.3 - - - +
124D GLU* 3.7 21.6 + - + -
125D VAL 4.8 0.8 + - - -
5F ILE* 3.7 29.7 - - + +
6F LYS* 1.3 89.3 - - - +
8F LEU* 1.3 66.4 + - - +
9F ASP* 3.3 5.5 + - - +
12F GLN* 4.0 17.9 - - + -
13F THR 4.0 5.2 - - - -
14F ARG* 3.4 66.2 + - + +
15F ILE* 2.9 32.0 + - + +
45F GLY 3.4 2.9 - - - +
46F VAL* 3.7 26.2 - - + -
89F PHE* 4.0 2.0 - - - -
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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