Contacts of the strand formed by residues 79 - 89 (chain G) in PDB entry 5M5X
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 GLY 79 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G TYR* 3.3 21.9 - - - -
74G ASN* 3.0 28.7 + - - +
77G VAL* 3.8 1.0 - - - +
78G GLY* 1.3 77.5 - - - +
80G VAL* 1.3 61.0 + - - -
81G VAL 3.9 0.9 + - - -
124G VAL* 3.7 11.6 - - - +
125G TRP 3.4 12.1 - - - -
126G GLN* 4.3 1.6 - - - -
127G PRO* 5.4 1.6 - - - -
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Residues in contact with VAL 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G MET* 3.6 23.6 - - + -
72G LYS 4.3 3.1 - - - -
73G TYR* 4.7 5.2 - - + +
79G GLY* 1.3 73.8 - - - -
81G VAL* 1.3 74.8 + - - +
82G LEU* 3.6 8.5 + - + +
124G VAL* 3.3 5.4 - - - +
125G TRP* 2.9 44.5 + - + +
153G PHE* 3.6 35.9 - - + -
243G VAL* 4.0 27.8 - - + -
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Residues in contact with VAL 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LEU* 3.7 33.9 - - + +
70G VAL* 3.7 12.5 - - + +
71G MET* 2.7 26.9 + - - +
72G LYS 3.8 10.7 + - - +
74G ASN* 4.6 15.0 - - + +
77G VAL* 5.0 5.8 - - + -
79G GLY 4.8 0.9 - - - +
80G VAL* 1.3 74.6 - - - +
82G LEU* 1.3 69.1 + - - +
83G GLY 3.3 24.7 - - - +
122G LEU* 3.8 31.0 - - + -
123G TYR 4.1 2.2 - - - -
124G VAL* 4.7 3.1 - - + +
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 5.7 2.5 - - + -
39D PHE* 3.2 16.9 - - - -
40D LEU* 4.0 5.9 - - + +
89D LEU* 3.2 23.0 - - - +
92D ILE* 3.7 33.7 - - + -
38G ILE* 3.9 25.1 - - + -
70G VAL* 4.8 1.1 - - - -
71G MET* 4.0 9.0 - - - -
80G VAL* 3.7 22.0 - - + +
81G VAL* 1.3 84.0 - - - +
83G GLY* 1.3 56.3 + - - +
123G TYR* 2.9 26.4 + - + +
125G TRP* 3.8 20.6 - - + +
153G PHE* 4.2 11.0 - - + -
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Residues in contact with GLY 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D PHE* 3.7 7.6 - - - -
43D PHE* 5.9 2.7 - - - -
89D LEU* 5.1 3.8 - - - -
66G LEU* 5.3 0.9 - - - +
70G VAL* 3.8 16.6 - - - +
81G VAL* 3.3 13.0 - - - +
82G LEU* 1.3 80.9 - - - +
84G TYR* 1.3 72.3 + - - +
122G LEU* 3.3 17.5 - - - +
123G TYR 4.3 0.6 + - - -
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Residues in contact with TYR 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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39D PHE* 3.0 17.2 - - - -
43D PHE* 3.0 53.3 - + + -
46D GLU* 3.6 17.2 + - - +
47D LYS* 3.6 23.7 - - + +
62G MET* 3.3 32.1 - - + +
66G LEU* 3.5 41.5 - - + -
70G VAL* 5.5 1.1 - - + -
83G GLY* 1.3 80.1 - - - +
85G GLU* 1.3 66.2 + - - +
87G LEU* 5.1 14.6 - - + -
120G VAL* 3.9 6.5 - - + -
121G ASN 3.2 11.4 - - - -
122G LEU* 3.6 8.5 - - + -
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Residues in contact with GLU 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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39D PHE* 3.9 17.9 - - + -
43D PHE* 4.1 18.5 - - + -
84G TYR* 1.3 82.1 - - - +
86G GLY* 1.3 81.2 + - - +
87G LEU 3.8 0.7 - - - -
120G VAL* 3.3 5.3 - - - +
121G ASN* 2.4 64.3 + - + +
123G TYR* 5.3 4.0 - - + -
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Residues in contact with GLY 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 5.4 1.4 - - - -
84G TYR* 5.4 0.4 - - - -
85G GLU* 1.3 94.5 + - - +
87G LEU* 1.3 54.1 + - - +
88G LYS* 2.7 21.4 + - - +
119G HIS 2.8 17.5 - - - +
120G VAL* 3.6 2.9 - - - -
121G ASN* 3.9 6.5 - - - -
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Residues in contact with LEU 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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1663A ALA 6.0 1.2 - - - -
58G LEU* 3.6 42.5 - - + +
61G VAL* 5.5 10.1 - - + -
62G MET* 3.7 34.1 - - + -
66G LEU* 5.0 10.3 - - + -
84G TYR* 5.1 13.0 - - + -
85G GLU 3.8 1.0 - - - -
86G GLY* 1.3 69.8 - - - +
88G LYS* 1.3 59.4 + - - +
89G ILE* 4.0 12.7 + - + +
118G CYS* 5.5 7.9 - - - -
119G HIS 4.5 1.1 - - - +
120G VAL* 5.1 9.6 - - + -
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Residues in contact with LYS 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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66F ARG* 5.1 12.5 - - - +
86G GLY* 2.7 15.2 + - - +
87G LEU* 1.3 71.1 - - - +
89G ILE* 1.3 71.5 + - - +
90G LEU* 3.8 24.2 - - - +
91G ASP 4.9 1.3 - - - +
103G LYS* 5.8 4.9 - - - +
118G CYS* 3.2 3.6 - - - +
119G HIS* 3.2 54.9 + - + +
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Residues in contact with ILE 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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1663A ALA 3.3 32.4 + - - +
57G PRO* 4.3 12.6 - - + -
58G LEU* 4.2 29.6 - - + +
61G VAL* 5.0 9.9 - - + -
87G LEU* 4.0 13.6 + - + +
88G LYS* 1.3 77.3 - - - +
90G LEU* 1.3 69.9 + - - +
91G ASP 3.5 0.2 + - - -
103G LYS* 3.4 25.0 - - + +
105G ILE* 4.1 14.4 - - + -
116G THR* 3.6 24.7 - - + +
117G TRP 4.0 1.8 - - - +
118G CYS* 3.6 12.6 - - + -
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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