Contacts of the helix formed by residues 138 - 147 (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 TYR 138 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ARG* 3.5 45.8 - - + +
93G ASP* 2.6 36.4 + - + +
96G GLY* 4.7 4.2 - - - -
98G GLY* 3.1 39.0 + - - -
99G TYR 3.3 19.7 - - - -
100G ILE* 3.9 17.5 - - + -
136G VAL* 3.2 3.9 + - + -
137G ASN* 1.3 70.6 - - - +
139G GLU* 1.3 67.5 + - + +
141G PHE* 3.8 7.2 - - - +
142G VAL* 3.0 33.0 + - + +
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Residues in contact with GLU 139 (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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98G GLY 4.4 0.9 + - - +
137G ASN* 3.0 9.4 + - - +
138G TYR* 1.3 84.1 - - + +
140G GLU* 1.3 64.4 + - - +
142G VAL* 3.1 26.8 - - + +
143G GLN* 3.2 26.0 + - + +
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Residues in contact with GLU 140 (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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137G ASN* 3.0 44.3 + - + +
139G GLU* 1.3 76.4 - - - +
141G PHE* 1.3 56.3 + - - +
143G GLN* 2.7 33.2 + - + +
144G MET* 2.9 49.5 + - + +
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Residues in contact with PHE 141 (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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897A TYR* 3.4 27.1 - + - -
90G ARG* 3.3 21.5 - - - -
105G LEU* 3.8 31.4 - - + -
124G MET* 4.2 15.9 - - + -
125G ILE* 5.8 0.4 - - + -
128G ALA* 3.4 32.8 - - + -
129G ASP 5.1 0.4 - - - -
136G VAL* 3.4 23.3 - - + -
137G ASN 3.1 18.0 + - - +
138G TYR* 3.8 7.4 - - - +
140G GLU* 1.3 77.2 - - - +
142G VAL* 1.4 58.9 + - - +
144G MET* 3.6 12.6 + - + +
145G MET* 3.2 36.0 + - + +
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Residues in contact with VAL 142 (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 ARG 4.0 15.5 - - - +
87G GLU* 5.2 1.3 - - - -
88G ALA* 3.3 31.4 - - + +
90G ARG* 3.3 23.6 - - + +
138G TYR* 3.0 18.3 + - + +
139G GLU* 3.1 30.3 - - + +
141G PHE* 1.4 71.6 - - - +
143G GLN* 1.3 60.1 + - + +
145G MET* 3.4 7.9 + - + +
146G THR* 2.8 37.9 + - + +
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Residues in contact with GLN 143 (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 ARG 5.3 0.7 - - - +
139G GLU* 3.2 27.5 + - + +
140G GLU* 2.7 38.0 + - + +
142G VAL* 1.3 78.9 - - + +
144G MET* 1.3 56.7 + - + +
146G THR* 3.3 6.8 + - - -
147G ALA* 2.9 31.2 + - - +
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Residues in contact with MET 144 (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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900A MET* 4.2 6.1 - - - +
127G GLU* 4.3 22.7 - - + +
128G ALA* 4.4 6.3 - - - -
129G ASP* 3.3 46.7 - - + +
140G GLU* 2.9 38.5 + - + +
141G PHE* 3.8 14.4 - - + +
142G VAL 3.4 0.2 - - - -
143G GLN* 1.3 72.3 - - - +
145G MET* 1.4 62.1 + - - +
146G THR 3.3 0.7 + - - -
147G ALA* 3.3 22.0 + - - +
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Residues in contact with MET 145 (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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893A LEU* 3.5 32.1 - - + +
896A CYS* 5.5 7.3 - - + +
897A TYR* 3.6 32.5 - - + -
900A MET* 3.5 31.8 - - + +
90G ARG* 3.9 11.7 - - - +
124G MET* 5.2 12.1 - - + -
127G GLU* 5.6 3.4 - - - -
141G PHE* 3.2 45.4 + - + +
142G VAL* 3.6 13.0 - - + +
143G GLN 3.4 0.2 - - - -
144G MET* 1.4 77.0 - - - +
146G THR* 1.3 68.6 + - + +
147G ALA 3.5 0.2 - - - -
148G LYS* 6.0 1.0 - - - -
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Residues in contact with THR 146 (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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893A LEU* 5.7 3.8 - - + -
896A CYS* 6.1 4.5 - - + -
42G ASN* 6.1 1.6 - - - +
85G ILE* 3.7 13.7 - - + +
86G ARG* 3.6 42.6 + - - +
87G GLU 5.8 0.4 - - - +
142G VAL* 2.8 22.5 + - + +
143G GLN* 3.3 9.4 + - - -
145G MET* 1.3 88.2 - - + +
147G ALA* 1.3 63.2 + - - +
148G LYS* 3.3 16.1 + - - +
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Residues in contact with ALA 147 (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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900A MET* 4.2 10.4 - - - +
143G GLN 2.9 17.7 + - - +
144G MET* 3.3 19.1 + - - +
146G THR* 1.3 71.0 - - - +
148G LYS* 1.4 64.2 + - - +
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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