Contacts of the helix formed by residues 87 - 98 (chain G) in PDB entry 4KYI
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 ASP 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58G GLN* 5.9 0.2 + - - -
85G GLY 3.3 5.6 + - - +
86G MET* 1.3 75.1 - - - +
88G ILE* 1.3 73.6 + - - +
89G LYS* 3.9 21.2 - - - +
90G ASP* 2.9 20.2 + - - +
91G ILE* 2.9 25.9 + - - +
129G GLN* 4.3 6.6 - - - +
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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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54G ILE* 4.8 11.4 - - + -
55G GLN* 4.3 26.2 - - + +
58G GLN* 3.6 49.4 - - + +
63G ILE* 6.3 0.7 - - + -
86G MET 3.7 1.4 + - - -
87G ASP* 1.3 82.1 + - - +
89G LYS* 1.3 66.7 + - + +
91G ILE* 3.1 15.3 + - + +
92G LYS* 3.0 25.8 + - + +
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Residues in contact with LYS 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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87G ASP* 3.9 15.2 + - - +
88G ILE* 1.3 84.2 - - + +
90G ASP* 1.3 73.4 + - - +
92G LYS* 3.6 6.4 + - - +
93G LYS* 3.5 43.6 + - + +
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Residues in contact with ASP 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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86G MET* 3.6 16.4 - - + -
87G ASP* 2.9 20.5 + - - +
89G LYS* 1.3 93.4 - - - +
91G ILE* 1.3 60.4 + - - +
93G LYS* 3.5 11.1 + - - +
94G LEU* 2.8 29.5 + - - +
128G MET* 5.1 0.9 - - - +
129G GLN* 4.0 15.1 + - - +
132G LYS* 4.1 14.7 + - - -
172G ASN* 4.7 4.8 - - - +
173G VAL* 3.6 27.4 - - + +
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Residues in contact with ILE 91 (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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51G LEU* 4.3 7.2 - - + -
54G ILE* 3.9 27.6 - - + -
63G ILE* 6.3 0.2 - - + -
81G ILE* 3.8 23.8 - - + +
82G LEU* 4.0 26.5 - - + -
86G MET* 3.4 37.7 - - + +
87G ASP 2.9 15.2 + - - +
88G ILE* 3.1 19.9 + - + +
90G ASP* 1.3 76.7 - - - +
92G LYS* 1.3 54.4 + - - +
94G LEU* 3.4 1.5 - - - +
95G ILE* 2.8 40.4 + - + +
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Residues in contact with LYS 92 (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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51G LEU* 4.0 11.0 - - + -
55G GLN* 3.4 31.6 - - + +
88G ILE* 3.0 17.5 + - + +
89G LYS* 3.9 6.5 - - - +
90G ASP 3.3 0.2 - - - -
91G ILE* 1.3 77.8 - - - +
93G LYS* 1.3 62.5 + - + +
96G GLU* 2.6 71.3 + - + +
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Residues in contact with LYS 93 (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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89G LYS* 3.5 34.3 + - - +
90G ASP* 3.5 19.3 + - - +
91G ILE 3.3 0.4 - - - -
92G LYS* 1.3 79.3 - - + +
94G LEU* 1.3 59.0 + - - +
96G GLU* 4.9 1.6 - - - -
97G GLY* 2.9 21.3 + - - +
172G ASN* 4.4 5.5 + - - +
173G VAL* 4.1 11.0 - - + -
174G ASP* 2.7 42.0 + - - +
177G ILE* 3.2 20.7 - - + +
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Residues in contact with LEU 94 (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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77G MET* 5.1 3.1 - - - -
81G ILE* 4.7 18.2 - - + -
86G MET* 4.1 15.7 - - + -
90G ASP 2.8 18.9 + - - +
91G ILE* 3.1 8.7 + - - +
93G LYS* 1.3 74.9 - - - +
95G ILE* 1.3 65.3 + - + +
98G LEU* 2.7 56.8 + - + +
125G ILE* 3.8 35.4 - - + -
173G VAL* 3.8 24.9 - - + +
176G ILE* 5.2 7.2 - - + -
177G ILE* 5.0 5.6 - - + -
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Residues in contact with ILE 95 (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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47G GLY* 3.4 32.8 - - - +
48G ILE* 3.3 20.4 - - + +
50G TYR 6.1 0.2 - - - -
51G LEU* 3.6 35.9 - - + +
54G ILE* 5.6 2.7 - - + -
77G MET* 4.8 16.2 - - - -
78G THR* 4.4 14.4 - - + +
81G ILE* 4.2 17.5 - - + -
91G ILE* 2.8 32.0 + - + +
94G LEU* 1.3 76.3 - - + +
96G GLU* 1.3 61.8 + - - +
98G LEU* 3.2 18.5 - - + +
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Residues in contact with GLU 96 (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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48G ILE* 4.8 11.0 - - + +
51G LEU* 4.1 18.4 - - + +
92G LYS* 2.6 56.6 + - + +
93G LYS* 4.7 1.9 - - - +
95G ILE* 1.3 80.5 - - + +
97G GLY* 1.3 64.0 + - - +
99G ASP* 3.8 14.0 - - - +
391G ARG* 5.4 7.6 + - - +
395G VAL* 5.6 4.5 - - + +
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Residues in contact with GLY 97 (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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93G LYS 2.9 20.5 + - - -
96G GLU* 1.3 79.9 - - - +
98G LEU* 1.3 57.1 + - - +
99G ASP* 3.0 18.5 + - - +
177G ILE* 4.2 26.9 - - - +
180G THR* 4.8 4.9 + - - -
181G LYS* 4.8 5.9 + - - -
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Residues in contact with LEU 98 (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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48G ILE* 4.5 5.5 - - - +
77G MET* 4.2 25.6 - - + -
94G LEU* 2.7 46.2 + - + +
95G ILE* 3.2 15.7 - - + +
97G GLY* 1.3 70.4 - - - +
99G ASP* 1.3 65.1 + - - +
100G ILE* 4.1 7.7 + - + +
103G LEU* 3.6 31.0 - - + -
118G PHE* 5.2 1.6 - - + -
121G ILE* 4.1 11.0 - - + -
122G LEU* 5.8 1.3 - - + -
125G ILE* 4.5 11.0 - - + -
176G ILE* 5.3 3.4 - - + +
177G ILE* 5.1 5.0 - - + +
180G THR* 3.8 25.8 - - + -
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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