Contacts of the strand formed by residues 119 - 127 (chain A) in PDB entry 5OAB
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ALA* 3.5 27.8 - - + -
48A PHE* 4.6 4.5 - - + -
106A CYS* 3.1 5.2 - - - -
107A ASP 2.8 40.3 + - - +
108A PRO 4.3 1.1 - - - +
109A PRO* 3.9 20.4 - - + -
113A ASP* 4.3 1.3 - - - +
114A PRO* 4.0 24.7 - - + +
116A TYR* 4.0 23.6 - - + -
118A LEU* 1.3 80.1 - - - +
120A PRO* 1.3 73.9 - - + +
121A VAL* 3.8 4.2 - - + +
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Residues in contact with PRO 120 (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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8A ALA* 3.4 23.0 - - - +
11A PHE* 3.5 36.3 - - + +
48A PHE* 3.8 22.8 - - + -
51A VAL* 4.1 16.4 - - + +
52A ALA* 4.0 16.2 - - - +
55A CYS* 3.8 14.8 - - - -
104A VAL* 4.6 4.0 - - + -
105A ALA 3.4 9.0 - - - +
106A CYS* 3.9 5.2 - - - -
119A VAL* 1.3 88.9 - - + +
121A VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 121 (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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7A LYS* 4.0 30.1 - - + +
8A ALA* 4.0 9.9 - - + +
11A PHE* 3.8 9.4 - - - -
68A ASN* 4.5 0.4 - - - +
105A ALA* 2.8 27.9 + - + +
106A CYS* 4.2 1.8 - - - -
107A ASP* 3.8 31.9 - - + +
108A PRO 5.9 0.4 - - - +
119A VAL* 3.8 11.2 - - + +
120A PRO* 1.3 78.9 - - - +
122A HIS* 1.3 78.9 + - + +
209A NA 2.7 26.0 - - - -
211A CL 3.9 1.2 - - - +
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Residues in contact with HIS 122 (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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0A MET 6.1 3.1 - - - -
1A TRP* 6.3 0.4 - + - -
7A LYS* 3.0 35.8 + - - -
11A PHE* 3.6 6.3 - - - -
64A ASN* 5.2 7.0 - - - -
66A ARG* 5.9 2.2 - - - -
68A ASN* 5.8 1.1 - - - -
104A VAL* 3.3 9.9 - - - +
105A ALA* 2.9 42.8 + - + -
121A VAL* 1.3 97.5 + - + +
123A LEU* 1.3 62.6 + - - +
124A ASP* 4.5 7.2 - - - +
202A PO4 2.8 34.0 + - - +
207A NA 4.5 1.6 - - - -
209A NA 4.4 3.4 - - - -
210A CL 3.4 19.8 - - + +
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Residues in contact with LEU 123 (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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11A PHE* 3.6 6.5 - - + -
15A HIS* 3.9 27.8 - - + +
42A THR* 3.7 37.7 - - + +
44A LEU* 4.5 12.1 - - + -
102A PHE* 3.8 20.0 - - + -
103A ILE 3.8 7.4 - - - +
104A VAL* 4.4 8.3 - - + -
122A HIS* 1.3 69.1 - - - +
124A ASP* 1.3 62.3 + - - +
125A SER 3.8 21.1 - - - +
126A ILE* 4.4 5.8 - - + -
202A PO4 2.8 33.2 + - - +
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Residues in contact with ASP 124 (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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62A CYS* 3.5 15.8 - - - +
63A LYS* 2.8 56.8 + - - +
64A ASN* 4.7 5.7 + - - +
69A CYS* 3.5 25.3 - - - -
103A ILE* 2.8 22.3 + - + +
105A ALA* 4.8 4.4 - - + +
122A HIS* 3.5 11.2 + - - +
123A LEU* 1.3 74.1 - - - +
125A SER* 1.3 65.8 + - - +
202A PO4 4.8 1.1 - - - -
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Residues in contact with SER 125 (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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63A LYS* 3.9 21.1 - - - +
102A PHE* 3.6 0.5 - - - -
103A ILE* 2.9 48.5 + - - +
123A LEU* 3.5 6.4 - - - +
124A ASP* 1.3 84.1 + - - +
126A ILE* 1.3 73.1 + - - +
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Residues in contact with ILE 126 (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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42A THR* 4.7 9.6 - - + +
78A MET* 3.9 20.9 - - + -
98A GLN* 3.9 24.9 - - - +
100A LYS* 3.7 24.7 - - + -
101A PHE 3.4 11.4 - - - +
102A PHE* 4.2 8.5 - - + +
103A ILE* 4.7 2.0 - - - +
123A LEU* 4.4 16.2 - - + -
125A SER* 1.3 87.6 + - - +
127A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 127 (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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71A GLN* 3.4 36.1 - - - +
100A LYS* 3.1 35.1 + - - +
101A PHE* 2.9 56.8 + - + +
103A ILE* 4.3 10.3 - - + -
126A ILE* 1.3 76.0 - - - +
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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