Contacts of the helix formed by residues 98 - 108 (chain G) in PDB entry 6IY6
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 SER 98 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23G ASP* 2.7 28.5 + - - -
24G TYR* 3.8 27.6 - - - -
25G ALA* 3.6 17.7 - - - +
29G TYR* 4.4 0.2 - - - -
93G VAL* 3.4 12.4 - - - +
97G ALA* 1.3 74.6 - - - +
99G LYS* 1.3 63.5 + - - +
100G GLN* 3.5 4.0 + - - -
101G MET* 3.5 14.0 + - - +
102G VAL* 3.4 18.4 + - - +
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Residues in contact with LYS 99 (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 VAL* 3.8 22.2 - - + -
98G SER* 1.3 73.8 - - - +
100G GLN* 1.3 67.4 + - - +
102G VAL* 3.5 5.0 + - - +
103G LYS* 2.9 27.6 + - - +
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Residues in contact with GLN 100 (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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23G ASP* 3.3 40.5 - - + +
29G TYR* 3.3 22.2 - - - +
98G SER* 3.5 4.5 + - - -
99G LYS* 1.3 80.5 + - - +
101G MET* 1.3 56.9 + - - +
103G LYS* 3.4 17.5 - - + +
104G PHE* 2.9 31.7 + - - +
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Residues in contact with MET 101 (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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25G ALA* 3.9 17.5 - - - -
28G ARG* 3.8 14.4 - - + +
29G TYR* 3.7 26.4 - - + -
91G VAL* 4.3 5.8 - - + -
97G ALA* 3.5 25.1 - - + -
98G SER* 3.5 19.6 + - - +
100G GLN* 1.3 76.1 - - - +
102G VAL* 1.3 55.2 + - - +
104G PHE* 3.3 4.0 + - - +
105G ALA* 2.8 34.9 + - - +
139G VAL* 4.5 7.2 - - + -
140G GLN 3.5 24.7 - - - +
141G LYS* 3.6 19.5 - - - -
142G ILE* 3.7 18.3 - - + +
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Residues in contact with VAL 102 (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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71G ALA* 5.6 1.8 - - + -
73G GLY 4.0 14.6 - - - +
74G LYS 3.9 13.5 - - - +
75G GLN 4.1 0.9 - - - +
76G CYS* 3.8 21.1 - - + +
91G VAL* 3.4 32.3 - - + +
92G ALA 4.5 0.2 - - - -
93G VAL* 3.6 21.1 - - + +
97G ALA* 4.8 0.4 - - + -
98G SER 3.4 13.6 + - - +
99G LYS 3.7 7.4 - - - +
101G MET* 1.3 72.7 - - - +
103G LYS* 1.3 65.2 + - - +
105G ALA* 3.5 7.9 - - - +
106G ALA* 3.2 23.7 + - - +
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Residues in contact with LYS 103 (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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99G LYS 2.9 17.9 + - - +
100G GLN* 3.4 17.7 - - + +
101G MET 3.3 0.2 - - - -
102G VAL* 1.3 78.6 - - - +
104G PHE* 1.3 60.7 + - - +
106G ALA* 3.5 4.7 + - - +
107G ASN* 3.1 47.2 + - - +
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Residues in contact with PHE 104 (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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29G TYR* 3.4 31.2 - + + -
30G GLY* 3.6 40.2 - - - -
31G ILE* 4.0 15.0 - - + -
100G GLN 2.9 19.2 + - - +
101G MET 3.3 3.6 + - - +
103G LYS* 1.3 72.2 - - - +
105G ALA* 1.3 60.3 + - - +
107G ASN* 3.1 13.4 + - + +
108G ILE* 3.0 41.3 + - + +
142G ILE* 4.2 11.4 - - + -
144G VAL* 3.9 23.6 - - + -
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Residues in contact with ALA 105 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69G SER* 4.5 0.3 - - - -
76G CYS* 3.9 14.8 - - - -
78G LEU* 3.9 19.0 - - + +
91G VAL* 3.9 23.8 - - + -
101G MET 2.8 20.7 + - - +
102G VAL* 3.5 8.7 - - - +
103G LYS 3.3 0.4 - - - -
104G PHE* 1.3 74.8 - - - +
106G ALA* 1.3 59.0 + - - +
108G ILE* 3.5 29.6 - - - +
142G ILE* 4.7 6.7 - - + -
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Residues in contact with ALA 106 (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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69G SER* 3.8 21.6 + - - +
71G ALA* 3.6 31.0 - - + -
76G CYS* 3.7 6.3 - - - -
102G VAL 3.2 12.2 + - - +
103G LYS* 3.9 4.9 - - - +
105G ALA* 1.3 76.3 - - - +
107G ASN* 1.3 65.1 + - - +
108G ILE 3.3 3.7 + - - +
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Residues in contact with ASN 107 (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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103G LYS* 3.1 47.9 + - - +
104G PHE* 3.1 17.9 + - + +
106G ALA* 1.3 77.9 - - - +
108G ILE* 1.3 62.9 + - - +
109G ASN* 3.1 15.1 - - - +
147G LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 108 (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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66G VAL* 3.7 25.7 - - + +
69G SER* 4.1 11.1 + - - -
78G LEU* 5.1 0.2 - - + -
104G PHE* 3.0 28.9 + - + +
105G ALA* 3.5 18.3 - - - +
106G ALA 3.3 7.5 - - - +
107G ASN* 1.3 75.5 - - - +
109G ASN* 1.3 72.5 + - - +
110G LYS* 4.9 0.2 - - - -
112G SER* 3.8 15.0 - - - -
114G VAL* 4.1 3.4 - - + -
142G ILE* 3.6 35.4 - - + -
144G VAL* 3.6 29.2 - - + -
147G LEU* 5.6 3.1 - - + -
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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