Contacts of the strand formed by residues 60 - 66 (chain B) in PDB entry 2F4W
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.3 11.7 - - + -
48B VAL 3.4 2.7 - - - -
49B ARG* 3.5 27.8 - - + -
58B GLY 4.2 1.3 - - - -
59B GLY* 1.3 78.3 - - - -
61B TYR* 1.3 59.9 + - - +
82B THR* 3.7 1.7 - - - +
146B SER* 3.1 20.3 + - - +
147B LEU* 3.4 18.4 - - + -
150B ASN* 2.7 34.3 + - - +
163B VAL* 3.8 22.7 - - + -
166B GLU* 2.8 46.9 + - + +
167B ILE* 3.8 19.3 - - + -
170B LYS* 3.8 31.5 + - + +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR* 3.8 4.6 - - - +
47B VAL* 3.3 5.8 - - - +
48B VAL* 2.7 54.8 + - + +
50B GLY* 4.2 4.5 - - - -
56B TYR* 3.5 39.9 + + + +
59B GLY* 3.7 19.3 - - - -
60B TYR* 1.3 77.2 - - - +
62B HIS* 1.3 61.6 + - - +
63B GLY 4.0 0.3 + - - -
80B MET* 3.9 21.8 - - + -
82B THR* 3.9 7.6 - - + -
83B PRO 3.9 10.1 - - - -
84B ASN* 3.6 34.7 + - + -
122B MET* 4.1 11.4 - - + -
139B LYS 4.3 2.3 + - - -
142B LEU 4.7 2.7 - - - -
143B ALA* 3.4 29.3 + - - +
146B SER* 4.5 6.5 - - - -
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Residues in contact with HIS 62 (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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45B HIS* 2.9 27.7 + + - +
46B TYR* 3.3 14.4 - - - -
47B VAL* 4.5 1.1 - - - +
60B TYR 4.1 0.4 - - - -
61B TYR* 1.3 72.9 - - - +
63B GLY* 1.3 63.8 + - - +
80B MET* 3.7 3.2 - - - +
81B ILE* 2.7 57.0 + - + +
82B THR* 3.0 24.7 + - - +
149B PHE* 5.9 0.2 - - - -
150B ASN* 3.8 9.4 + - - +
153B ASP* 3.6 25.8 + - - -
155B VAL* 4.7 3.7 - - + +
156B PHE* 3.9 31.6 - + + +
160B PHE* 4.0 16.9 - + - -
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Residues in contact with GLY 63 (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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45B HIS* 3.4 9.0 + - - +
46B TYR* 2.9 43.1 + - - +
62B HIS* 1.3 78.0 - - - +
64B LYS* 1.3 62.0 + - - +
79B TYR 3.2 14.4 - - - -
80B MET* 3.8 0.2 - - - -
81B ILE* 3.8 11.7 - - - -
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Residues in contact with LYS 64 (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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43B GLU* 2.8 35.7 + - + +
44B TRP 3.2 12.8 - - - +
45B HIS* 4.3 12.7 + - + +
46B TYR* 3.3 10.6 - - - -
63B GLY* 1.3 74.9 - - - +
65B LEU* 1.3 59.7 - - - +
66B ILE* 4.1 20.7 - - + +
78B ILE* 3.7 1.6 - - - -
79B TYR* 2.9 54.3 + - + +
81B ILE* 4.0 18.4 - - + -
90B ASN* 5.9 2.0 - - - +
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Residues in contact with LEU 65 (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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42B LEU 3.8 0.7 - - - +
43B GLU* 3.4 4.3 - - - +
44B TRP* 2.8 37.1 + - + +
46B TYR* 4.1 15.3 - - + -
64B LYS* 1.3 77.6 - - - +
66B ILE* 1.3 63.3 + - - +
67B PHE* 3.7 25.5 - - + -
76B PRO* 4.4 4.3 - - + -
77B SER 3.3 4.3 - - - +
78B ILE* 3.7 36.8 - - + -
111B VAL* 3.8 24.5 - - + -
114B ILE* 4.4 13.5 - - + -
115B LEU* 3.8 25.4 - - + -
118B LEU* 5.4 0.2 - - + -
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Residues in contact with ILE 66 (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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40B ASN* 6.3 0.7 - - - +
42B LEU* 3.4 7.2 - - + +
43B GLU* 4.2 17.5 - - + +
64B LYS* 4.1 26.0 - - + +
65B LEU* 1.3 77.7 - - - +
67B PHE* 1.3 68.9 + - - +
68B PRO* 3.9 1.7 - - - +
76B PRO* 3.2 3.9 - - - +
77B SER* 2.8 43.8 + - - +
79B TYR* 3.8 27.6 - - + +
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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