Contacts of the helix formed by residues 102 - 112 (chain G) in PDB entry 2DFS
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 ALA 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100G ILE 3.9 0.2 + - - -
101G SER* 1.3 72.0 - - - +
103G ALA* 1.4 57.5 + - - +
105G LEU* 3.6 14.4 - - + +
106G ARG* 3.0 31.3 + - - +
125G ILE* 6.0 5.8 - - + -
130G ILE* 4.0 18.1 - - + +
134G GLY* 3.1 18.2 + - - +
135G GLN* 4.7 0.6 - - - +
136G VAL* 4.8 2.4 - - + +
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Residues in contact with ALA 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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101G SER* 3.2 12.2 + - - +
102G ALA* 1.4 76.7 - - - +
104G GLU* 1.3 56.5 + - + +
106G ARG* 3.3 7.2 + - - +
107G HIS* 2.9 29.7 + - - +
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Residues in contact with GLU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G PHE* 3.3 58.1 - - + +
100G ILE* 3.7 9.5 - - + +
101G SER* 2.6 46.1 + - - +
103G ALA* 1.3 78.3 - - + +
105G LEU* 1.3 61.1 + - - +
107G HIS* 3.4 4.9 + - - +
108G VAL* 3.1 20.8 + - - +
135G GLN* 5.7 0.3 + - - -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A TYR* 3.9 11.7 - - - +
90G ARG* 3.5 27.4 - - - +
100G ILE* 4.0 11.3 - - + +
101G SER 3.0 16.0 + - - +
102G ALA* 3.6 8.7 - - + +
104G GLU* 1.3 74.1 - - - +
106G ARG* 1.3 64.9 + - - +
108G VAL* 3.3 10.2 - - + +
109G MET* 3.2 29.2 + - + +
121G VAL* 5.5 6.3 - - + -
124G MET* 6.2 0.2 - - + -
125G ILE* 4.7 17.3 - - + -
136G VAL* 4.5 17.0 - - + -
141G PHE* 3.8 37.7 - - + -
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Residues in contact with ARG 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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102G ALA 3.0 19.7 + - - +
103G ALA* 3.3 6.5 + - - +
105G LEU* 1.3 71.7 - - - +
107G HIS* 1.4 60.2 + - - +
109G MET* 3.3 2.6 + - - -
110G THR* 2.8 44.5 + - + +
118G ASP* 2.7 47.7 + - - +
121G VAL* 3.9 23.2 - - + +
122G ASP* 2.6 46.0 + - - -
125G ILE* 3.9 13.7 - - - +
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Residues in contact with HIS 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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20F ASP 4.0 0.7 - - - -
21F LYS* 2.8 43.5 + - - +
22F ASP* 4.2 3.4 + - - -
92G PHE* 3.3 27.1 - + - -
103G ALA 2.9 17.7 + - - +
104G GLU* 3.6 7.4 - - - +
106G ARG* 1.4 74.7 - - - +
108G VAL* 1.3 63.5 + - - +
110G THR* 4.2 4.0 - - - -
111G ASN* 2.9 66.8 + - + +
112G LEU* 3.8 17.8 + - + +
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Residues in contact with VAL 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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890A ILE* 3.9 20.8 - - + +
894A GLN* 3.8 3.3 + - - -
89G PHE* 3.2 41.3 - - + -
90G ARG* 5.2 3.8 - - - +
91G VAL* 5.9 1.1 - - + +
92G PHE* 3.9 15.5 - - + -
100G ILE* 5.5 2.5 - - + -
104G GLU 3.1 17.5 + - - +
105G LEU* 3.3 24.2 - - + +
107G HIS* 1.3 81.4 - - - +
109G MET* 1.3 67.9 + - + +
112G LEU* 3.4 28.5 + - + +
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Residues in contact with MET 109 (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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890A ILE* 4.3 3.8 - - + +
893A LEU* 4.2 9.6 - - + -
894A GLN* 2.9 33.2 + - + +
897A TYR* 3.5 42.4 - - + +
89G PHE* 4.1 25.1 - - + -
90G ARG* 5.9 1.3 - - - +
105G LEU* 3.2 23.6 + - + +
106G ARG 3.9 2.2 - - - +
108G VAL* 1.3 89.3 - - + +
110G THR* 1.3 58.8 + - - +
115G LYS* 3.7 0.3 - - - -
116G LEU* 2.9 37.6 + - + +
121G VAL* 3.9 20.4 - - + -
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Residues in contact with THR 110 (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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106G ARG* 2.8 35.0 + - + +
107G HIS* 4.1 2.9 + - - -
109G MET* 1.3 72.6 - - - +
111G ASN* 1.4 60.5 + - - +
112G LEU 3.7 0.2 - - - -
115G LYS* 3.3 23.6 - - - +
116G LEU 3.3 22.4 - - - +
117G THR 3.9 9.4 - - - +
118G ASP* 4.1 17.1 + - - +
121G VAL* 3.8 22.9 - - + -
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Residues in contact with ASN 111 (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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17F SER* 3.2 37.5 + - - -
18F LEU* 5.0 1.6 - - - +
20F ASP* 3.7 5.1 + - - -
21F LYS 5.2 0.4 - - - -
23F GLY* 5.4 7.7 - - - +
107G HIS* 2.9 46.3 + - + +
110G THR* 1.4 80.8 + - - +
112G LEU* 1.3 63.5 + - - +
115G LYS* 3.3 26.1 + - - +
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Residues in contact with LEU 112 (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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887A LEU* 4.5 7.0 - - + -
890A ILE* 3.6 30.5 - - + -
894A GLN* 2.8 28.6 + - - -
17F SER 3.7 7.0 - - - +
18F LEU* 3.7 43.3 - - + +
21F LYS* 5.9 1.3 - - + -
91G VAL* 6.2 3.1 - - + -
92G PHE* 5.1 5.2 - - + -
107G HIS* 3.8 24.7 - - + +
108G VAL* 3.4 24.0 + - + +
111G ASN* 1.3 87.2 - - - +
113G GLY* 1.3 58.1 + - - +
115G LYS* 3.3 7.5 + - - +
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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