Contacts of the helix formed by residues 95 - 105 (chain G) in PDB entry 4QOC
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 GLU 95 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92G SER* 3.2 31.4 + - - +
94G LYS* 1.3 78.0 - - + +
96G HIS* 1.3 60.5 + - - +
97G ARG 3.4 3.1 - - - -
98G LYS* 3.3 44.7 + - + +
99G ILE* 3.1 28.4 + - - +
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Residues in contact with HIS 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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19G ILE* 3.5 20.7 - - + +
93G VAL 3.0 19.5 + - - -
94G LYS* 3.3 11.1 + - - -
95G GLU* 1.3 70.1 - - - +
97G ARG* 1.3 66.7 + - - +
99G ILE* 3.1 3.8 + - + +
100G TYR* 2.9 28.4 + - - -
201G 35T 2.7 79.0 + + + -
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Residues in contact with ARG 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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55C PHE* 4.9 6.7 - - + -
59C GLN* 3.3 13.8 + - - +
201C 35T 3.0 86.9 + - + +
18G GLN* 4.0 29.8 - - + +
19G ILE* 3.9 22.2 - - + -
95G GLU 3.4 0.4 - - - -
96G HIS* 1.3 76.7 - - - +
98G LYS* 1.3 63.5 + - - +
100G TYR* 3.2 2.5 + - - -
101G THR* 3.1 24.3 + - - -
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Residues in contact with LYS 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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201C 35T 3.6 31.0 - - + -
95G GLU* 3.3 42.7 + - + +
96G HIS 3.2 0.2 - - - -
97G ARG* 1.3 78.3 - - - +
99G ILE* 1.3 62.9 + - + +
101G THR* 3.2 6.3 + - - -
102G MET* 3.2 32.5 + - + +
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Residues in contact with ILE 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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54G LEU* 4.9 0.2 - - + -
86G PHE* 5.1 1.1 - - + -
91G PHE* 4.1 6.7 - - + -
92G SER 3.4 23.1 - - - +
93G VAL* 4.1 9.9 - - - +
95G GLU 3.1 13.8 + - - +
96G HIS 3.1 7.2 + - - +
98G LYS* 1.3 77.3 - - + +
100G TYR* 1.3 61.6 + - - +
102G MET* 3.1 23.6 + - + +
103G ILE* 3.0 38.5 + - + +
201G 35T 3.6 66.9 - - + -
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Residues in contact with TYR 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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55C PHE* 4.1 8.3 - + - -
59C GLN* 3.5 17.3 - - - +
19G ILE* 3.6 35.0 - - + +
23G GLU* 3.7 32.8 - - + +
24G GLN* 2.6 35.8 + - - -
50G MET* 3.9 20.4 - - + -
54G LEU* 3.6 19.1 - - + +
96G HIS 2.9 24.1 + - - -
97G ARG 3.6 6.7 - - - +
99G ILE* 1.3 76.1 - - - +
101G THR* 1.3 57.6 + - - +
103G ILE* 3.1 8.2 + - + +
104G TYR* 2.9 36.5 + + + -
201G 35T 3.7 16.5 - + + -
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Residues in contact with THR 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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59C GLN* 3.2 17.3 + - - -
62C MET* 3.7 37.3 - - + +
63C THR* 5.3 4.1 - - + +
201C 35T 3.8 14.4 - - + -
97G ARG 3.1 13.9 + - - -
98G LYS* 3.5 11.0 - - - -
99G ILE 3.2 0.2 - - - -
100G TYR* 1.3 78.0 - - - +
102G MET* 1.3 63.8 + - + +
103G ILE 3.4 0.3 + - - -
104G TYR* 3.5 4.4 + - - +
105G ARG* 3.5 24.6 + - + +
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Residues in contact with MET 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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86G PHE* 3.6 54.0 - - + +
88G VAL* 3.9 21.8 - - + -
91G PHE* 3.8 27.6 - - + -
98G LYS* 3.2 14.1 + - + +
99G ILE* 3.1 33.9 + - + +
101G THR* 1.3 78.8 - - + +
103G ILE* 1.3 60.3 + - - +
105G ARG* 3.5 17.9 + - - +
106G ASN* 3.0 22.2 - - - +
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Residues in contact with ILE 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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34G LEU* 5.0 5.4 - - + -
50G MET* 4.1 14.6 - - + -
53G VAL* 4.4 10.8 - - + -
54G LEU* 3.6 31.9 - - + -
57G LEU* 3.8 17.7 - - + -
86G PHE* 4.0 20.6 - - + -
99G ILE* 3.0 28.0 + - + +
100G TYR* 3.6 14.6 - - + +
102G MET* 1.3 74.1 - - - +
104G TYR* 1.3 59.8 + - - +
105G ARG 3.1 2.0 - - - -
106G ASN* 2.9 25.7 + - - +
107G LEU* 3.5 27.1 - - + +
201G 35T 5.1 0.2 - - + -
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Residues in contact with TYR 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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65A ARG* 3.9 8.4 + - - -
40C SER 5.1 1.3 - - - -
41C VAL* 2.7 44.1 + - + +
55C PHE* 4.3 3.6 - - - -
56C TYR* 4.5 0.2 - - - -
59C GLN* 3.4 34.3 - - + -
63C THR* 3.9 22.3 - - + +
23G GLU* 2.5 32.5 + - - -
26G THR* 4.8 0.9 + - - +
28G VAL* 5.3 0.4 - - + -
50G MET* 3.9 14.2 - - + +
100G TYR* 2.9 30.1 + - + +
101G THR 3.5 3.3 + - - +
102G MET 3.5 0.2 - - - -
103G ILE* 1.3 75.4 - - - +
105G ARG* 1.3 60.5 + - - +
106G ASN 3.0 1.6 + - - -
107G LEU* 3.4 38.9 - - + +
109G VAL* 3.9 15.3 - - + -
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Residues in contact with ARG 105 (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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65A ARG* 3.2 41.3 + - - +
68A ASP* 5.2 9.5 + - - +
63C THR* 5.5 0.9 - - + +
31G LYS* 3.1 22.6 + - - +
84G ASP 4.6 2.0 + - - -
85G LEU 3.4 10.3 + - - -
86G PHE 2.9 36.4 + - - -
87G GLY* 3.4 9.1 - - - +
101G THR* 3.5 16.5 + - + +
102G MET* 3.5 19.2 + - - +
103G ILE 3.1 0.8 - - - -
104G TYR* 1.3 77.8 - - - +
106G ASN* 1.3 63.2 + - - +
107G LEU 3.6 0.2 - - - -
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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