Contacts of the strand formed by residues 81 - 90 (chain G) in PDB entry 4JCQ
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 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G LEU* 5.0 0.9 - - + -
53G ILE* 3.4 12.1 - - + +
55G ILE* 3.7 31.4 - - + -
74G ILE* 3.8 33.9 - - + +
77G ILE* 3.9 22.4 - - + -
79G PRO 3.5 10.7 + - - +
80G THR* 1.3 79.1 - - - +
82G LYS* 1.3 71.6 + - - +
83G VAL* 4.3 6.7 - - + -
100G ALA* 3.5 19.1 - - + +
101G GLU 4.9 0.2 + - - -
104G ASN* 3.6 11.4 + - - +
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Residues in contact with LYS 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G PRO* 4.0 27.5 - - + +
53G ILE 2.8 12.5 + - - +
54G THR* 3.4 16.1 - - + +
55G ILE* 2.8 32.2 + - - -
80G THR* 4.0 8.6 + - + +
81G VAL* 1.3 76.8 - - - +
83G VAL* 1.3 58.2 + - - +
104G ASN* 3.5 32.5 + - + +
106G PHE* 4.1 22.0 - - + -
189G LEU* 4.4 17.7 - - + +
190G LYS 4.5 16.4 - - - -
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Residues in contact with VAL 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ILE* 3.3 16.6 - - + +
57G ILE* 4.0 18.6 - - + -
74G ILE* 5.2 2.9 - - + -
81G VAL* 4.2 7.6 + - + -
82G LYS* 1.3 78.6 - - - +
84G VAL* 1.3 59.0 + - - +
96G ILE 4.8 3.6 - - - +
97G TYR* 3.4 45.3 - - + +
100G ALA* 3.8 21.5 - - + +
104G ASN 3.0 7.8 + - - +
105G ARG* 3.8 12.3 - - + -
106G PHE* 2.8 36.1 + - - +
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Residues in contact with VAL 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G THR* 4.0 22.9 - - + -
55G ILE 2.7 9.2 + - - +
56G PHE* 3.4 29.0 - - + -
57G ILE 2.9 25.3 + - - -
82G LYS 5.4 0.2 - - - -
83G VAL* 1.3 78.1 - - - +
85G GLY* 1.3 66.7 + - - +
86G THR* 3.7 1.6 + - - +
97G TYR* 4.4 1.8 - - - -
106G PHE* 3.4 6.3 - - + +
107G SER* 4.5 3.1 - - - -
108G LEU* 3.7 35.2 - - + +
183G ILE* 4.6 5.4 - - + -
189G LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ILE 3.7 7.0 - - - -
84G VAL* 1.3 73.3 - - - +
86G THR* 1.3 59.3 + - - -
89G VAL* 3.9 10.3 - - - -
97G TYR* 3.6 8.6 - - - -
106G PHE 3.0 13.1 + - - -
107G SER* 3.6 0.9 + - - -
108G LEU* 2.9 26.7 + - - +
111G THR* 3.4 9.1 + - - -
113G TYR* 3.4 16.4 - - - -
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Residues in contact with THR 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ASP 4.7 0.7 + - - -
69F THR* 2.8 44.3 + - + +
72F ASP* 4.8 1.0 + - - +
73F MET* 5.7 0.2 - - - -
27G TYR* 4.2 9.0 - - + +
56G PHE* 4.5 6.5 - - + -
57G ILE 2.9 26.8 + - - +
58G ASN* 3.2 24.6 - - + +
84G VAL 4.1 6.3 - - - +
85G GLY* 1.3 75.9 - - - -
87G GLY* 1.3 61.9 + - - +
88G TRP 3.0 9.5 + - - +
108G LEU* 3.8 25.0 - - + +
111G THR* 3.3 9.4 - - - +
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Residues in contact with GLY 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLU* 3.5 30.6 - - - +
68F ASP* 4.2 7.2 - - - +
69F THR* 3.7 2.2 - - - +
58G ASN* 3.8 1.3 - - - -
86G THR* 1.3 70.8 + - - +
88G TRP* 1.3 63.0 + - - +
110G ASN 3.4 19.6 + - - +
111G THR* 3.2 6.4 + - - -
112G ARG* 3.1 22.9 + - - +
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Residues in contact with TRP 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLN* 3.4 13.4 - - - +
65F GLU* 3.5 37.4 - - + +
131F ILE* 4.9 8.1 - - + -
58G ASN* 3.1 28.1 + - - -
59G SER 2.8 34.2 + - - -
60G GLN* 3.6 33.4 - - + +
86G THR 3.0 3.6 + - - -
87G GLY* 1.3 74.2 - - - +
89G VAL* 1.3 68.6 + - - +
111G THR* 4.1 0.9 - - - -
112G ARG* 3.3 44.2 - - + +
167G TRP* 3.6 35.0 - + + -
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Residues in contact with VAL 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ILE* 3.6 26.7 - - + +
59G SER 3.4 3.1 - - - +
85G GLY* 3.9 12.8 - - - -
88G TRP* 1.3 80.1 - - - +
90G ALA* 1.3 59.5 + - - +
93G GLY* 3.5 29.8 - - - +
94G ILE* 3.5 17.8 - - + +
97G TYR* 3.9 13.5 - - + -
111G THR* 4.3 2.5 - - + -
112G ARG 3.0 6.6 + - - -
113G TYR* 3.3 30.0 - - + -
114G MET 3.1 21.0 + - - -
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G SER 2.9 7.7 + - - +
60G GLN* 3.7 16.6 - - + +
61G GLY 3.4 9.0 + - - -
89G VAL* 1.3 76.5 - - - +
91G SER* 1.3 64.4 + - - +
92G ALA 3.2 1.0 + - - -
93G GLY* 2.8 24.6 + - - -
94G ILE* 3.8 2.9 - - - -
114G MET* 3.2 19.7 - - + +
167G TRP* 3.7 27.1 - - + -
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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