Contacts of the strand formed by residues 84 - 89 (chain G) in PDB entry 4GEK
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 LYS 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58G THR 3.2 5.1 + - - -
59G GLN* 3.2 33.9 + - + +
60G VAL* 3.0 24.1 + - - +
83G CYS* 1.3 78.4 - - - +
85G ILE* 1.3 76.4 + - - +
86G ILE* 4.4 7.1 - - + +
109G THR* 3.9 0.9 - - - -
110G PRO* 3.6 26.7 - - + +
112G ASP* 2.7 34.5 + - - +
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Residues in contact with ILE 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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60G VAL* 3.3 27.4 - - + +
62G ASP* 4.8 2.9 - - + -
71G THR* 3.7 41.1 - - + +
74G VAL* 3.9 7.4 - - + -
75G ARG* 3.6 44.4 - - + +
78G ILE* 4.2 5.2 - - + -
84G LYS* 1.3 77.9 - - - +
86G ILE* 1.3 71.5 + - - +
109G THR* 3.9 12.8 - - + -
110G PRO 3.0 9.5 + - - +
111G VAL* 3.2 8.5 - - + +
112G ASP 2.9 25.8 + - - -
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Residues in contact with ILE 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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59G GLN* 3.7 24.9 - - + +
60G VAL 2.8 10.2 + - - +
61G TYR* 3.3 43.3 - - + +
62G ASP 2.8 31.4 + - - +
84G LYS* 4.4 15.7 - - + +
85G ILE* 1.3 77.9 - - - +
87G ALA* 1.3 55.9 + - - +
88G ILE* 3.8 21.3 + - + +
112G ASP* 3.5 10.1 - - + +
114G ILE* 3.8 28.5 - - + -
121G ILE* 5.4 1.1 - - + -
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Residues in contact with ALA 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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62G ASP* 3.5 6.3 - - - -
65G CYS* 3.7 19.0 - - + -
71G THR* 3.6 22.9 - - + +
85G ILE 4.0 0.6 - - - -
86G ILE* 1.3 71.2 - - - +
88G ILE* 1.3 61.2 + - - +
98G CYS* 4.8 4.0 - - - -
111G VAL* 4.0 16.6 - - + -
112G ASP 2.9 7.2 + - - +
113G VAL* 3.4 8.8 - - + +
114G ILE 2.8 26.9 + - - +
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Residues in contact with ILE 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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61G TYR* 4.3 2.9 - - + -
62G ASP 3.0 9.4 + - - +
63G LEU* 3.9 13.5 - - + -
64G GLY 2.8 29.5 + - - -
65G CYS* 3.0 7.6 + - - -
86G ILE* 3.8 23.3 - - + +
87G ALA* 1.3 78.4 - - - +
89G ASP* 1.3 64.2 + - - +
114G ILE* 3.3 17.7 - - + +
116G GLY* 3.4 28.0 - - - +
117G ASP 4.6 1.3 - - - +
118G ILE* 4.3 15.5 - - + +
121G ILE* 3.3 46.7 - - + -
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Residues in contact with ASP 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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65G CYS* 3.4 11.2 + - - -
66G SER* 2.9 18.1 + - - +
88G ILE* 1.3 75.4 - - - +
90G ASN* 1.3 60.7 + - - +
91G SER* 3.0 22.3 + - - -
94G MET* 4.2 8.3 - - + -
95G ILE* 3.4 22.4 - - + +
114G ILE 3.2 4.2 + - - -
115G GLU* 3.3 10.0 - - - -
116G GLY 3.0 20.6 + - - -
303G GEK 2.7 59.5 + - - -
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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