Contacts of the strand formed by residues 46 - 51 (chain E) in PDB entry 2Y6T
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 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42E ALA* 3.7 15.4 - - + +
43E GLU* 3.7 37.8 - - + +
44E LYS 3.2 6.3 + - - +
45E GLY* 1.3 82.2 - - - +
47E SER* 1.3 60.9 + - - +
99E VAL* 5.7 3.6 - - + -
100E MET 3.9 9.0 - - - +
101E ASP* 3.1 31.2 - - - +
145E TYR* 4.7 7.9 - - + -
146E VAL 3.3 33.9 - - - +
147E PRO* 3.8 6.7 - - + -
148E GLN* 4.1 7.5 - - - +
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Residues in contact with SER 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 4.3 4.7 - - - -
46E MET* 1.3 75.5 - - - +
48E ARG* 1.3 59.2 + - - +
49E GLN* 3.3 28.3 + - - +
144E VAL 3.9 0.9 - - - +
145E TYR* 3.8 2.9 - - - +
146E VAL* 2.8 37.7 + - - +
148E GLN* 4.4 17.1 + - - +
168F VAL* 4.8 13.2 - - - +
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.5 36.0 - - - +
34E GLU* 4.4 6.2 + - - +
39E TYR* 3.1 13.2 + - - -
40E PRO 2.9 22.0 + - - -
41E GLN* 3.5 24.3 + - - +
42E ALA* 4.3 10.0 - - + +
47E SER* 1.3 73.7 - - - +
49E GLN* 1.3 60.9 + - - +
50E VAL* 4.4 2.0 - - + -
143E VAL* 3.9 11.4 - - + -
144E VAL 3.7 3.1 - - - +
145E TYR* 3.3 38.1 + - + -
168F VAL* 3.4 9.7 - - - +
169F LYS 3.1 57.9 + - - +
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Residues in contact with GLN 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E SER* 3.3 19.4 + - - +
48E ARG* 1.3 76.6 - - - +
50E VAL* 1.3 64.3 + - - +
51E ILE* 5.9 0.2 - - - -
142E ILE 3.8 0.5 - - - +
143E VAL* 4.5 0.2 - - - +
144E VAL* 2.8 44.5 + - - +
146E VAL* 3.8 3.4 - - + +
148E GLN 5.4 0.2 + - - -
150E VAL 3.0 26.9 + - - -
151E GLU* 3.9 4.6 - - - +
152E VAL* 3.1 50.2 + - + +
166F ALA* 4.0 17.5 - - + +
167F GLN 3.6 4.9 - - - +
168F VAL* 4.0 19.8 - - + +
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Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.9 23.6 - - + -
48E ARG* 4.4 3.8 - - - -
49E GLN* 1.3 80.3 - - - +
51E ILE* 1.3 66.4 + - - +
52E PHE* 3.8 25.5 + - + -
141E PRO* 3.8 28.0 - - + -
142E ILE 3.4 4.0 - - - +
143E VAL* 4.1 11.7 - - + -
166F ALA* 3.5 4.3 - - - +
167F GLN* 2.9 32.4 + - - +
169F LYS* 3.7 24.7 - - + -
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Residues in contact with ILE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLN 5.9 0.2 - - - -
50E VAL* 1.3 77.0 - - - +
52E PHE* 1.3 71.2 + - - +
53E LEU* 4.0 17.5 - - + +
64E VAL* 5.1 0.7 - - + -
66E LEU* 3.8 27.8 - - + -
140E LEU 4.8 0.3 - - - +
141E PRO* 3.5 8.3 - - - +
142E ILE* 3.0 49.1 + - + +
144E VAL* 5.1 1.6 - - + -
152E VAL* 4.3 14.1 - - + -
154E TYR* 3.5 54.3 - - + -
166F ALA* 3.8 11.0 - - + +
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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