Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 2JJ6
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 HIS 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 4.9 10.9 + - - +
101A PHE* 3.1 5.8 - - - -
102A VAL* 2.9 31.4 + - - +
103A ASP 3.6 9.9 + - - -
104A GLY* 1.3 88.3 + - - +
106A GLN* 1.3 68.9 + - - +
107A LEU* 3.4 3.3 + - - +
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Residues in contact with GLN 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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77A PRO* 5.4 2.1 - - - +
99A ARG* 3.6 34.1 - - + +
100A VAL 3.5 6.7 - - - +
101A PHE* 3.4 18.0 - - + -
105A HIS* 1.3 76.8 - - - +
107A LEU* 1.3 69.6 + - - +
108A PHE* 3.2 20.6 - - - +
109A ASP* 3.1 26.3 + - - -
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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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59A LEU* 4.1 11.9 - - + -
75A ALA 4.6 2.6 - - - +
76A ILE* 4.7 2.5 - - + -
77A PRO* 3.7 41.9 - - + +
78A TYR* 3.7 33.4 - - + +
80A PRO* 3.5 29.4 - - + -
100A VAL 2.9 10.1 + - - +
102A VAL* 3.5 31.6 - - + -
105A HIS 3.4 3.3 + - - +
106A GLN* 1.3 82.7 + - - +
108A PHE* 1.3 77.6 + - + +
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Residues in contact with PHE 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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50A LEU* 3.8 13.5 - - + -
59A LEU* 3.6 28.3 - - + -
61A ARG* 3.5 65.5 - - + +
75A ALA 4.2 3.1 - - - +
76A ILE* 4.2 5.2 - - + -
100A VAL* 2.9 62.5 + - + -
106A GLN* 3.2 14.3 + - - +
107A LEU* 1.3 96.6 - - + +
109A ASP* 1.3 70.8 + - - +
110A PHE* 5.1 3.1 - - + -
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Residues in contact with ASP 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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61A ARG* 4.9 2.8 + - - -
73A GLN* 4.1 9.9 - - - +
97A ARG* 3.8 15.2 + - - -
98A PHE 3.3 6.5 - - - +
99A ARG* 2.8 50.1 + - - +
106A GLN* 3.1 14.3 + - - +
108A PHE* 1.3 88.1 - - - +
110A PHE* 1.3 63.2 + - - +
111A TYR* 4.0 22.7 + - + -
71B GLU* 4.9 5.4 - - - +
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Residues in contact with PHE 110 (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 ALA 3.2 22.9 - - - -
48A ILE* 3.5 33.4 - - + -
61A ARG* 3.8 17.5 - - + -
62A ASN* 3.7 31.2 - - - -
73A GLN* 3.6 15.5 - - - -
97A ARG* 3.8 1.8 - - - -
98A PHE* 2.8 42.6 + + + +
100A VAL* 5.4 0.2 - - + -
108A PHE* 5.0 5.4 - - + -
109A ASP* 1.3 75.0 - - - +
111A TYR* 1.3 77.6 + - - +
112A HIS* 3.6 0.8 + - - -
113A ARG* 3.5 47.8 - - + -
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Residues in contact with TYR 111 (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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73A GLN* 5.1 0.8 + - - -
96A PRO* 3.4 31.2 - - + +
97A ARG* 2.9 45.8 + - + -
109A ASP* 4.0 14.7 + - + -
110A PHE* 1.3 85.9 - - - +
112A HIS* 1.3 68.2 + - - +
113A ARG* 3.4 15.8 + - - +
69B ARG 5.6 0.2 - - - -
70B GLY* 4.1 7.4 - - - -
71B GLU* 3.3 72.1 + - + +
72B GLU 5.5 0.3 + - - -
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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