Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 1Q2L
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 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 4.0 21.3 - - + -
46A ALA* 4.5 1.1 - - + -
47A ILE 3.4 5.2 - - - +
48A ARG* 3.4 40.2 - - + +
52A GLY 3.6 0.6 + - - +
53A MET* 1.3 72.1 - - - +
55A VAL* 1.3 63.3 + - - +
231A MET 3.7 4.0 + - - -
232A LYS* 3.4 33.2 - - + +
233A ALA 3.3 19.2 + - - -
419A MET* 3.4 17.4 - - + +
424A VAL* 4.3 20.4 - - + -
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.3 4.8 - - - -
47A ILE* 2.9 41.8 + - + +
49A LEU* 3.6 35.0 - - + -
53A MET* 3.9 14.1 - - - +
54A VAL* 1.3 79.1 - - - +
56A LEU* 1.3 66.6 + - - +
57A LEU* 3.7 22.5 + - + -
233A ALA* 3.3 20.9 - - + +
235A ILE* 4.3 12.1 - - + -
248A ALA* 4.4 7.2 - - + -
252A PHE* 4.7 2.5 - - + -
419A MET* 4.2 2.0 - - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.1 26.5 - - + -
44A TYR* 4.6 5.6 - - + -
45A GLN 4.0 8.7 - - - +
46A ALA* 4.5 0.9 - - + +
55A VAL* 1.3 72.1 - - - +
57A LEU* 1.3 69.2 + - - +
58A VAL* 3.7 20.6 + - + -
233A ALA 2.8 10.8 + - - +
234A VAL* 3.5 8.5 - - + +
235A ILE 3.1 23.6 + - - -
415A LEU* 4.4 15.5 - - + -
419A MET* 3.8 21.9 - - + +
424A VAL* 4.4 9.6 - - + -
427A THR* 3.9 29.6 - - + +
428A LEU* 4.8 6.1 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.4 5.2 - - - +
45A GLN* 2.8 48.1 + - - +
47A ILE* 3.6 24.7 - - + -
55A VAL* 4.1 18.6 - - + +
56A LEU* 1.3 72.4 - - - +
58A VAL* 1.3 61.5 + - - +
235A ILE* 3.9 13.7 - - + -
241A LEU* 3.5 20.7 - - + +
244A LEU* 3.5 33.7 - - + +
245A ALA* 3.5 35.7 - - + +
248A ALA* 4.3 2.5 - - + -
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.5 6.7 - - + -
43A GLN 3.4 3.8 - - - +
44A TYR* 3.5 43.3 - - + -
56A LEU* 3.9 22.2 - - + +
57A LEU* 1.3 76.6 - - - +
59A SER* 1.3 61.2 + - - +
60A ASP 3.7 0.3 + - - -
234A VAL* 4.5 7.4 - - + -
235A ILE 3.1 10.1 + - - +
236A TYR* 3.5 38.4 - - + -
237A SER 3.2 24.9 + - - +
244A LEU* 3.7 4.2 - - - +
415A LEU* 4.7 4.3 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG 3.7 1.0 - - - -
43A GLN* 2.7 53.2 + - - +
57A LEU 4.0 1.2 - - - -
58A VAL* 1.3 72.1 - - - +
60A ASP* 1.3 58.9 + - - +
61A PRO* 3.5 15.5 - - - +
237A SER 3.4 4.7 + - - -
238A ASN 4.5 0.3 + - - -
239A LYS 2.6 29.8 + - - -
240A PRO* 3.8 4.0 - - - +
241A LEU* 3.9 17.2 - - - +
244A LEU* 4.3 1.3 - - - -
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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