Contacts of the strand formed by residues 52 - 57 (chain A) in PDB entry 3UMZ
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 GLY 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 1.3 76.3 - - - +
53A LYS* 1.3 60.7 + - - -
54A ASN* 3.1 12.0 + - - -
79A GLU* 3.5 6.0 - - - -
80A ILE 2.9 38.7 + - - -
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Residues in contact with LYS 53 (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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51A LEU 4.4 0.2 + - - -
52A GLY* 1.3 70.7 - - - -
54A ASN* 1.3 62.4 + - - +
55A VAL* 3.7 6.7 + - + +
63A SER* 3.9 5.4 + - - -
77A GLU* 3.1 39.5 - - + +
78A ILE 4.0 3.4 - - - -
79A GLU* 3.4 33.8 + - + +
90A ARG* 5.2 4.2 - - - +
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Residues in contact with ASN 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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48A PRO 4.3 2.1 - - - +
49A LEU* 3.5 25.4 - - + +
50A HIS* 2.9 49.9 + - - +
52A GLY 3.1 9.1 + - - -
53A LYS* 1.3 70.3 - - - +
55A VAL* 1.3 64.0 + - - +
56A VAL* 3.6 3.7 + - - +
63A SER* 3.4 19.7 + - - -
64A VAL* 5.1 1.3 - - + -
77A GLU* 3.5 2.3 - - - +
78A ILE* 2.9 44.2 + - + +
80A ILE* 3.5 10.7 - - - +
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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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53A LYS* 4.6 5.4 - - + +
54A ASN* 1.3 71.2 - - - +
56A VAL* 1.3 70.5 + - - +
62A CYS* 3.5 18.4 - - + +
63A SER* 3.1 19.2 + - - +
64A VAL 2.9 24.1 + - - -
74A GLN* 3.7 35.4 - - + +
76A ALA 3.8 9.9 - - - +
77A GLU* 3.8 24.0 - - + +
92A CYS* 6.0 1.3 - - - -
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Residues in contact with VAL 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 LEU* 4.8 0.4 - - + -
54A ASN* 4.2 7.6 - - + +
55A VAL* 1.3 77.3 - - - +
57A GLY* 1.3 60.5 + - - +
64A VAL* 3.4 25.1 - - + +
66A LEU* 3.7 28.5 - - + -
71A ILE* 5.2 0.2 - - + -
74A GLN 3.9 0.7 - - - -
75A HIS* 2.8 28.6 + - + +
76A ALA* 2.8 27.8 + - + +
78A ILE* 4.7 12.3 - - + -
123A PHE* 4.1 36.6 - - + -
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Residues in contact with GLY 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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56A VAL* 1.3 76.9 - - - +
58A ARG* 1.3 57.6 + - - -
59A MET 3.3 2.6 + - - -
62A CYS* 3.6 7.9 - - - -
64A VAL 3.1 9.1 + - - +
65A ALA* 3.4 3.5 - - - -
66A LEU 2.8 28.9 + - - -
71A ILE* 3.9 10.5 - - - -
72A SER 3.4 12.6 - - - -
73A LYS 3.4 10.3 - - - -
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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