Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 4YBH
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PRO* 5.1 1.2 - - - +
47A GLN* 1.3 74.0 - - - +
49A LEU* 1.3 59.1 + - - +
100A GLN 3.8 1.2 - - - +
101A ALA* 3.5 1.6 - - - -
102A MET* 3.0 63.7 + - + +
103A ASN 5.2 3.6 + - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A CYS* 4.0 6.1 - - - -
41A ALA* 3.7 25.6 - - + -
42A PRO* 5.3 0.2 - - + -
47A GLN* 3.7 27.6 + - + +
48A ARG* 1.3 75.1 - - - +
50A GLU* 1.3 65.1 + - - +
51A TRP* 4.1 24.0 - - + +
66A PRO* 5.8 9.6 - - + +
78A VAL* 4.6 8.7 - - + -
82A GLY* 3.7 29.4 - - - +
99A CYS* 4.3 0.9 - - - -
100A GLN 3.2 9.6 - - - +
101A ALA* 3.9 12.3 - - + -
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Residues in contact with GLU 50 (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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49A LEU* 1.3 78.1 - - - +
51A TRP* 1.3 67.2 + - - +
52A LYS* 3.5 23.8 + - + +
63A VAL* 3.7 38.4 - - + +
64A LEU 5.8 0.2 - - - +
98A ARG 3.6 0.9 - - - +
99A CYS* 3.4 3.3 - - - -
100A GLN* 3.0 45.7 + - + +
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Residues in contact with TRP 51 (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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36A LEU* 3.3 38.1 - - + -
37A LYS 3.9 8.1 - - - -
38A CYS* 3.7 10.1 - - + -
49A LEU* 4.1 8.3 - - + -
50A GLU* 1.3 72.9 - - - +
52A LYS* 1.3 63.5 + - - +
53A LEU* 5.6 1.8 - - + -
63A VAL* 3.5 7.6 - - - +
64A LEU* 3.0 47.9 + - + +
78A VAL* 3.8 22.0 - - + -
82A GLY 2.8 19.7 + - - -
83A SER 4.3 0.6 - - - -
84A LEU* 3.7 30.9 - - + +
97A PHE* 4.2 20.0 - + + -
98A ARG 3.3 23.1 - - - -
99A CYS* 3.4 35.6 - - + -
113A TYR* 4.1 7.2 - + - -
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Residues in contact with LYS 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 GLU* 3.5 26.4 + - + +
51A TRP* 1.3 78.8 - - - +
53A LEU* 1.3 60.9 + - - +
61A TRP* 3.7 20.8 - - + -
62A LYS 3.5 6.5 - - - +
63A VAL* 4.1 21.1 - - + -
98A ARG* 2.7 48.2 + - + +
100A GLN* 6.0 0.9 - - - -
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Residues in contact with LEU 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 TRP* 5.6 1.8 - - + -
52A LYS* 1.3 74.8 - - - +
54A ASN* 1.3 61.2 + - - +
55A THR* 4.5 4.5 - - + -
58A THR* 3.8 26.2 - - + -
60A ALA 3.4 0.7 - - - +
61A TRP* 3.4 7.4 - - - -
62A LYS* 2.9 41.3 + - + +
64A LEU* 3.8 35.9 - - + -
72A TRP* 5.4 2.7 - - + +
76A ALA* 5.2 0.2 - - + -
84A LEU* 4.2 4.9 - - + -
96A ILE 3.1 12.1 - - - +
97A PHE* 3.8 33.7 - - + -
411A ACT 4.0 17.3 - - + +
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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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53A LEU* 1.3 76.3 - - - +
55A THR* 1.3 66.1 + - - +
58A THR* 3.6 0.4 + - - -
59A GLU* 3.8 2.5 - - - -
60A ALA* 3.1 36.0 + - - +
61A TRP* 3.7 43.2 - - + +
95A GLY* 3.3 4.5 - - - -
96A ILE* 2.9 32.4 + - + +
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Residues in contact with THR 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 LEU* 4.2 3.6 - - + -
54A ASN* 1.3 86.4 - - - +
56A GLY* 1.3 60.0 + - - +
57A ARG 3.1 7.5 + - - -
58A THR* 3.1 11.4 + - - +
59A GLU* 2.9 26.9 + - - -
92A GLN 3.5 8.3 - - - -
93A ASP 3.6 5.8 - - - +
94A GLU 3.4 10.3 - - - +
97A PHE* 3.5 37.0 - - + -
411A ACT 2.7 30.3 + - - +
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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