Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 3U1J
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 LEU 51 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP* 1.3 75.5 - - - +
52A THR* 1.3 59.3 + - - +
25B ILE* 4.1 13.0 - - + -
26B LYS 3.4 15.7 - - - +
27B GLN* 3.2 40.8 - - + +
36B VAL* 4.4 2.0 - - + -
52B VAL 4.9 0.9 - - - +
53B THR* 3.4 46.2 - - + -
56B ALA* 4.0 13.9 - - + -
57B VAL 2.9 8.0 + - - +
58B LEU* 3.4 23.5 - - + -
59B THR* 2.7 33.1 + - - -
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Residues in contact with THR 52 (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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50A ASP 4.1 2.9 + - - +
51A LEU* 1.3 73.1 - - - +
53A VAL* 1.3 73.7 + - - +
25B ILE* 3.4 2.3 - - - +
26B LYS* 2.8 48.1 + - - +
33B LYS* 4.0 22.2 + - - +
58B LEU* 5.8 0.2 - - - -
59B THR* 3.4 30.1 - - - +
60B HIS* 6.4 0.2 - - - -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 1.3 85.1 - - - +
54A GLU* 1.3 63.5 + - - +
18B LEU* 3.7 35.2 - - + -
23B TYR* 3.9 12.3 - - + -
24B ARG 3.2 10.3 - - - +
25B ILE* 4.1 7.4 - - + -
26B LYS* 4.9 1.3 - - - +
46B PHE* 3.8 30.3 - - + -
58B LEU* 4.6 15.3 - - + -
59B THR 4.5 2.2 + - - +
60B HIS* 3.7 24.1 + - + -
65B LEU* 6.5 0.2 - - + -
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Residues in contact with GLU 54 (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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53A VAL* 1.3 78.3 - - - +
55A LYS* 1.3 71.3 + - - +
56A ALA 3.5 0.2 + - - -
23B TYR* 3.5 4.5 - - - -
24B ARG* 2.8 65.6 + - + +
26B LYS* 3.0 37.3 + - + +
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Residues in contact with LYS 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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54A GLU* 1.3 80.2 - - - +
56A ALA* 1.3 62.2 + - - +
57A ALA 3.5 15.9 - - - +
58A ASP* 2.7 35.7 + - - -
19B GLU* 4.4 11.8 - - + +
20B GLU 2.8 18.5 + - - +
21B GLY* 4.1 1.3 - - - -
22B VAL 3.7 7.4 - - - +
23B TYR* 3.3 37.8 - - + +
24B ARG* 5.4 0.5 + - - -
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Residues in contact with ALA 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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54A GLU 3.5 0.4 + - - +
55A LYS* 1.3 75.5 - - - +
57A ALA* 1.3 59.2 + - - +
22B VAL 2.8 16.2 + - - +
24B ARG* 3.9 24.5 - - + +
100B VAL* 3.8 30.3 - - + -
106B PRO* 3.3 19.3 - - + +
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Residues in contact with ALA 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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55A LYS* 3.5 12.8 - - - +
56A ALA* 1.3 79.4 - - + +
58A ASP* 1.3 67.6 + - - +
22B VAL* 2.7 44.9 + - + +
98B ILE* 4.3 9.4 - - + -
100B VAL* 5.0 0.7 - - + -
106B PRO* 3.8 22.2 - - + -
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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