Contacts of the strand formed by residues 105 - 111 (chain A) in PDB entry 2JDC
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 LEU 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.8 26.0 - - + -
65A GLN 3.5 24.7 - - - +
68A LYS 3.7 1.0 + - - -
69A GLN* 3.4 22.2 - - + +
70A TYR* 3.0 24.8 + - - +
98A LEU* 5.3 0.3 - - - +
103A ALA* 3.6 4.5 - - - +
104A ASP* 1.3 82.8 + - + +
106A LEU* 1.3 62.4 + - - +
107A TRP* 3.6 33.0 - - + -
142A TYR* 4.2 16.8 - - + -
143A LYS 3.4 13.0 - - - +
144A ARG* 3.9 15.0 - - - +
145A ILE* 3.7 6.2 - - - +
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Residues in contact with LEU 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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56A PHE* 3.9 35.9 - - + -
70A TYR* 3.4 15.7 - - - +
72A LEU* 4.0 15.0 - - + +
91A ILE* 4.4 18.6 - - + +
94A ALA* 5.5 0.2 - - + -
95A GLU* 4.4 11.4 - - + +
98A LEU* 3.9 21.8 - - + -
105A LEU* 1.3 73.4 - - - +
107A TRP* 1.3 60.6 + - - +
123A PHE* 3.7 28.3 - - + -
142A TYR* 3.2 1.9 - - - +
143A LYS* 2.7 41.8 + - + +
145A ILE* 4.7 7.4 - - + +
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Residues in contact with TRP 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 ALA* 2.9 32.1 + - + -
60A GLU 5.0 0.4 - - - -
61A HIS* 3.8 32.5 - + + +
64A LEU* 3.5 19.7 - - + -
69A GLN* 3.6 11.4 + - + -
70A TYR 2.9 25.6 + - - -
71A GLN* 3.3 51.3 - - + -
72A LEU* 2.9 26.7 + - - +
105A LEU* 3.6 16.8 - - + -
106A LEU* 1.3 76.1 - - - +
108A CYS* 1.3 73.8 + - - +
109A ASN* 3.8 20.2 - - - -
123A PHE* 4.7 1.1 - - - -
140A LEU* 3.5 16.6 - - + -
141A MET 3.2 11.9 - - - +
142A TYR* 3.9 1.1 - - + +
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Residues in contact with CYS 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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72A LEU* 3.6 35.0 - - + +
73A ARG* 5.6 0.4 - - - -
107A TRP* 1.3 84.4 - - - +
109A ASN* 1.3 74.8 + - - +
110A ALA* 3.1 12.5 + - + +
118A TYR* 3.8 29.2 - - + -
123A PHE* 4.9 5.8 - - + -
140A LEU* 3.6 1.2 - - - -
141A MET* 2.8 35.4 + - + +
1147A CAO 4.2 7.0 - - - -
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Residues in contact with ASN 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 HIS* 4.9 3.8 + - - -
71A GLN* 4.4 10.4 - - - +
72A LEU 4.8 1.8 + - - -
107A TRP* 3.8 21.0 - - - -
108A CYS* 1.3 71.0 - - - +
110A ALA* 1.3 60.6 + - - +
130A PHE* 3.6 32.7 - - + -
138A HIS* 3.2 21.1 - - + -
139A ILE 3.8 4.0 - - - -
140A LEU* 3.6 23.2 - - - +
1147A CAO 3.4 10.2 + - - -
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Residues in contact with ALA 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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108A CYS* 3.1 6.3 + - - +
109A ASN* 1.3 73.9 - - - +
111A ARG* 1.3 68.0 + - - +
118A TYR* 3.7 31.4 - - + -
138A HIS* 3.0 5.6 - - - -
139A ILE* 2.8 44.7 + - + +
141A MET* 3.7 17.9 - - + -
1147A CAO 3.9 7.2 - - - -
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Residues in contact with ARG 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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19A ILE 4.4 5.3 + - - -
20A LEU* 2.9 46.7 + - - +
110A ALA* 1.3 75.8 - - - +
112A THR* 1.3 65.7 + - - +
113A SER* 3.7 16.8 - - - +
114A ALA* 2.9 16.2 + - + +
115A SER 3.4 6.8 + - - -
135A VAL* 3.6 21.0 + - - +
137A PRO 3.6 7.9 - - - +
138A HIS* 3.6 10.2 + - + +
1147A CAO 3.5 41.2 + - + +
1148A SO4 2.8 43.2 + - - +
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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