Contacts of the helix formed by residues 122 - 128 (chain B) in PDB entry 2FMT
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 PRO 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B HIS* 3.1 31.2 - - + +
111B GLY 3.3 6.8 - - - +
112B SER* 3.3 20.4 - - - -
117B TRP* 3.3 31.2 - - + +
119B GLY 4.3 2.5 - - - +
120B ALA 3.4 7.6 - - - +
121B ALA* 1.3 88.7 - - - +
123B ILE* 1.3 72.5 + - + +
124B GLN* 4.8 0.9 - - - +
125B ARG* 4.3 0.4 - - + -
126B SER* 3.1 22.5 + - - -
134B THR* 4.6 0.2 + - - -
168B TYR* 5.5 0.7 - - - +
204B ALA* 4.2 2.7 - - + -
586D FME 4.1 15.3 - - + -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 4.8 3.4 - - + -
111B GLY* 3.4 19.7 - - - +
121B ALA 3.4 0.4 - - - -
122B PRO* 1.3 74.1 - - + +
124B GLN* 1.3 73.1 + - - +
126B SER* 2.5 26.8 + - - -
127B LEU* 3.2 3.5 + - - +
134B THR* 4.7 2.5 - - + +
164B SER* 4.5 2.9 - - - +
167B LEU* 3.8 28.9 - - + -
168B TYR* 3.0 59.2 - - + +
171B LEU* 3.6 25.1 - - + -
586D FME 4.5 11.9 - - + -
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 3.7 20.1 - - - +
123B ILE* 1.3 74.7 - - - +
125B ARG* 1.3 54.7 + - - +
127B LEU* 2.9 7.9 + - - +
128B TRP* 2.7 35.8 + - - +
164B SER* 3.1 34.2 - - - +
168B TYR* 3.5 31.0 + - - -
207B LEU* 3.7 36.0 - - + +
229B ALA* 3.7 6.4 - - + +
233B TRP* 5.5 2.4 + - - +
76D A 4.4 15.4 + - - -
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.9 15.2 - - + -
121B ALA 2.7 21.4 + - - +
122B PRO 4.3 1.1 - - - +
124B GLN* 1.3 79.2 - - - +
126B SER* 1.3 63.5 + - - +
128B TRP* 3.3 40.5 - - + +
129B ALA* 2.9 26.2 + - - +
204B ALA* 3.6 26.9 - - + -
205B GLU* 2.8 36.9 + - - +
206B LYS 3.6 3.4 - - - -
207B LEU* 2.9 43.4 - - - +
211B GLU* 2.5 37.2 + - - -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 3.3 27.1 - - - +
122B PRO 3.1 17.8 + - - -
123B ILE* 2.5 19.5 + - - -
125B ARG* 1.3 78.7 - - - +
127B LEU* 1.3 66.5 + - - +
129B ALA 3.3 4.2 + - - -
131B ASP* 3.2 32.3 + - - +
133B GLU 4.5 0.4 - - - -
134B THR* 3.5 18.8 + - - -
158B ILE* 3.5 16.6 - - - +
167B LEU* 4.3 1.2 - - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE 4.1 0.9 - - - +
124B GLN* 2.9 8.0 + - - +
126B SER* 1.3 79.1 + - - +
128B TRP* 1.3 66.7 + - - +
130B GLY* 3.1 10.3 + - - -
131B ASP 4.9 2.0 - - - +
158B ILE* 3.5 27.4 - - + -
159B THR 5.0 0.2 - - - +
162B ASP 3.5 9.4 - - - +
163B THR* 3.1 38.6 - - - +
164B SER* 4.0 2.9 - - - +
167B LEU* 3.6 21.3 - - + -
225B ARG* 3.6 10.0 - - - +
228B ARG* 3.9 28.0 - - + +
229B ALA* 4.2 18.6 - - + +
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Residues in contact with TRP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B TRP* 5.1 4.5 - + - -
124B GLN 2.7 16.3 + - - +
125B ARG* 3.3 54.1 - - + +
127B LEU* 1.3 72.3 - - - +
129B ALA* 1.3 78.7 + - + +
207B LEU* 5.8 0.2 - - + -
211B GLU* 3.8 14.9 + - + +
222B GLN* 3.4 31.4 + - - -
225B ARG* 3.0 29.3 - - - +
226B CYS* 3.6 29.7 - - - -
229B ALA* 3.6 14.5 - - + +
230B PHE* 3.8 16.1 - + + -
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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