Contacts of the strand formed by residues 44 - 49 (chain A) in PDB entry 4UY4
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 ARG 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLY 5.4 0.2 - - - +
43A CYS* 1.3 74.7 - - - +
45A ILE* 1.3 61.6 + - - +
60A LYS* 4.0 26.1 - - - +
61A GLY 3.3 10.0 + - - +
62A THR* 3.1 31.7 + - - -
79A ASP* 3.3 29.9 + - - -
100A ILE* 3.8 0.3 - - - -
101A LEU* 2.8 45.0 + - + +
103A GLU* 3.3 37.3 + - + +
104A ARG 4.2 17.9 + - - +
105A VAL* 4.6 8.7 - - + +
106A PRO* 5.8 3.2 - - - +
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Residues in contact with ILE 45 (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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40A ILE* 4.9 2.5 - - + -
43A CYS* 4.1 5.8 - - + +
44A ARG* 1.3 79.8 + - - +
46A GLN* 1.3 64.3 + - - +
47A HIS* 4.1 12.6 - - + -
60A LYS* 3.3 4.5 - - - +
61A GLY* 2.8 46.6 + - - +
63A VAL* 3.8 25.8 - - + -
76A ILE* 4.4 5.8 - - + -
78A TYR* 4.1 10.8 - - + +
89A LEU* 4.0 24.9 - - + -
98A LEU* 4.0 13.9 - - + -
99A GLU 3.5 8.5 - - - +
100A ILE* 3.9 23.1 - - + -
101A LEU* 4.1 5.3 - - - +
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Residues in contact with GLN 46 (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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45A ILE* 1.3 77.1 - - - +
47A HIS* 1.3 66.4 + - - +
58A GLN* 4.6 6.5 - - - +
59A TRP 3.1 13.2 - - - +
60A LYS* 3.6 27.0 + - + +
97A ALA 3.8 1.4 - - - +
98A LEU* 3.9 0.7 - - - +
99A GLU* 2.9 66.2 + - + +
101A LEU* 3.6 23.1 - - + +
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Residues in contact with HIS 47 (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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45A ILE* 4.1 8.1 - - + -
46A GLN* 1.3 78.0 - - - +
48A GLY* 1.3 76.1 + - - +
49A TRP* 3.8 13.9 - + - -
58A GLN* 3.3 8.7 + - - +
59A TRP* 2.9 62.6 + + + +
78A TYR* 2.8 33.6 + + - -
87A LEU* 4.8 0.2 - - + -
89A LEU* 4.4 2.3 - - + +
95A VAL* 3.6 21.4 - - + +
96A LEU 3.6 12.1 - - - +
97A ALA 4.0 4.0 - - - -
98A LEU* 3.8 29.8 - - + -
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Residues in contact with GLY 48 (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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47A HIS* 1.3 87.8 + - - +
49A TRP* 1.3 58.8 + - - -
56A VAL* 4.7 6.7 - - - -
57A GLU 3.5 11.0 - - - -
58A GLN* 3.6 14.1 - - - +
94A ARG 3.4 2.1 - - - +
96A LEU* 2.9 36.6 + - - -
97A ALA* 4.8 1.6 + - - +
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Residues in contact with TRP 49 (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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47A HIS* 3.8 22.0 - + - -
48A GLY* 1.3 72.3 - - - -
50A LYS* 1.3 60.1 + - - +
51A GLU* 2.9 37.9 + - + -
55A PRO 4.3 2.8 - - - +
56A VAL* 3.7 6.5 - - - +
57A GLU* 3.1 41.1 + - + +
59A TRP* 3.3 60.3 - + + +
87A LEU* 4.6 7.0 - - + +
94A ARG* 3.3 44.9 - - + +
95A VAL* 4.3 6.9 - - + +
228A ILE* 4.9 13.0 - - + -
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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