Contacts of the strand formed by residues 103 - 109 (chain A) in PDB entry 2J51
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 ASN 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.8 27.4 - - + +
65A ILE 3.2 5.0 - - - +
66A ASP* 3.3 29.6 + - - +
98A PHE 3.5 1.9 - - - +
99A TYR* 3.4 8.4 - - - -
100A TYR 3.0 32.3 + - - +
101A GLU* 3.5 16.9 + - - +
102A ASN* 1.3 80.1 - - - +
104A LEU* 1.3 59.9 + - - +
105A TRP* 3.8 11.2 + - - +
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Residues in contact with LEU 104 (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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24A VAL* 4.0 28.9 - - + -
63A LYS 3.5 3.6 - - - +
64A VAL* 3.5 0.2 - - - -
65A ILE* 2.9 46.2 + - + +
67A THR* 4.1 11.7 - - + +
73A LEU* 5.0 13.9 - - + +
76A TYR* 3.4 43.1 - - + -
77A MET* 6.1 1.3 - - - -
80A ILE* 5.0 4.9 - - + -
97A ALA* 4.9 1.3 - - + -
98A PHE 3.4 14.6 - - - +
99A TYR* 4.6 6.1 - - + +
103A ASN* 1.3 71.6 - - - +
105A TRP* 1.3 67.5 + - - +
106A ILE* 4.0 21.5 + - + -
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Residues in contact with TRP 105 (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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29A ASN* 5.7 0.4 - - - -
30A PRO* 3.4 34.9 - - + +
31A GLU* 3.5 38.4 - - + -
34A TRP* 5.5 7.2 - - + -
36A ILE* 4.0 23.8 - - + -
62A ALA* 4.4 16.4 - - + -
63A LYS 3.2 4.0 - - - -
64A VAL* 3.8 37.9 - - + +
97A ALA* 3.0 10.3 - - - +
98A PHE* 2.7 45.6 + - + +
100A TYR* 4.7 7.8 + + + +
103A ASN* 3.9 23.3 - - + +
104A LEU* 1.3 77.0 - - - +
106A ILE* 1.3 60.9 + - - +
107A LEU* 4.1 13.7 - - + -
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Residues in contact with ILE 106 (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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61A ALA 3.4 3.5 - - - +
62A ALA* 3.5 0.9 - - - -
63A LYS* 2.9 60.3 + - + +
65A ILE* 4.2 14.6 - - + -
76A TYR* 5.2 2.0 - - + -
79A GLU* 4.4 12.3 - - - +
80A ILE* 3.4 30.7 - - + -
83A LEU* 4.1 5.2 - - + -
94A LEU* 3.6 24.2 - - + -
96A ASP 3.8 2.2 - - - -
97A ALA* 4.5 0.2 - - - +
104A LEU* 4.1 15.7 - - + +
105A TRP* 1.3 77.0 - - - +
107A LEU* 1.3 60.9 + - - +
108A ILE* 3.8 21.0 + - + +
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Residues in contact with LEU 107 (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 TRP* 3.3 55.6 - - + -
51A ALA* 4.0 10.5 - - + -
60A ALA* 3.9 13.9 - - + -
61A ALA 3.4 2.5 - - - -
62A ALA* 4.0 10.5 - - + -
94A LEU* 3.6 4.7 - - - +
95A LEU* 2.7 35.9 + - + -
96A ASP* 2.8 37.2 + - + +
98A PHE* 4.0 14.8 - - + -
105A TRP* 4.3 18.8 - - + -
106A ILE* 1.3 76.3 - - - +
108A ILE* 1.3 57.0 + - - +
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Residues in contact with ILE 108 (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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60A ALA* 3.3 4.0 - - - -
61A ALA* 2.9 30.2 + - + +
63A LYS* 3.5 33.9 - - + -
79A GLU* 5.1 1.8 - - - +
83A LEU* 4.3 17.5 - - + -
92A VAL* 3.4 35.0 - - + -
93A LYS 3.4 7.4 - - - +
94A LEU* 4.9 0.4 - - + -
95A LEU* 3.8 3.6 - - - -
106A ILE* 3.8 19.5 - - + +
107A LEU* 1.3 78.3 - - - +
109A GLU* 1.3 69.7 + - - +
110A PHE 3.2 0.5 + - - -
173A ASP 6.2 1.1 - - - +
1314A DKI 3.6 31.2 - - - +
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Residues in contact with GLU 109 (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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59A LEU 5.3 0.2 - - - +
91A ILE 3.8 1.6 - - - +
92A VAL* 3.7 6.1 - - + +
93A LYS* 2.8 58.2 + - - +
95A LEU* 3.5 24.4 - - + +
108A ILE* 1.3 70.6 - - - +
110A PHE* 1.3 60.7 + - - +
111A CYS* 4.1 2.1 - - - -
170A LYS* 3.6 37.1 + - + +
1314A DKI 2.8 28.6 + - - -
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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