Contacts of the helix formed by residues 122 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A HIS* 3.1 32.5 - - + +
111A GLY 3.2 18.2 - - - +
112A SER* 3.4 8.5 - - - -
117A TRP* 3.2 24.2 - - + +
119A GLY 4.0 4.3 - - - +
120A ALA 3.5 5.6 - - - +
121A ALA* 1.3 88.9 - - - +
123A ILE* 1.3 75.1 + - + +
124A GLN* 4.7 0.7 - - - +
125A ARG 4.0 0.7 - - - -
126A SER* 3.1 22.0 + - - -
134A THR* 4.6 0.3 + - - -
168A TYR* 5.5 0.4 - - - +
204A ALA* 3.6 9.2 - - + -
585C FME 4.1 15.5 - - + -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 4.6 6.5 - - + -
111A GLY* 3.5 20.9 - - - +
121A ALA 3.4 0.2 - - - -
122A PRO* 1.3 79.6 - - + +
124A GLN* 1.3 68.4 + - + +
126A SER* 2.6 26.6 + - - -
127A LEU* 3.3 4.2 + - - +
134A THR* 4.8 2.5 - - - +
164A SER* 4.5 2.2 - - - +
167A LEU* 3.8 27.5 - - + +
168A TYR* 3.1 59.7 - - + +
171A LEU* 3.7 23.8 - - + -
585C FME 4.3 11.2 - - + -
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA* 3.5 27.3 - - + +
123A ILE* 1.3 74.1 - - - +
125A ARG* 1.3 57.5 + - - +
127A LEU* 3.3 3.3 + - - +
128A TRP* 2.8 31.2 + - - +
164A SER* 3.0 35.1 - - - +
168A TYR* 3.7 30.5 + - - -
207A LEU* 4.1 28.9 - - + +
229A ALA* 3.7 16.1 - - + +
233A TRP 5.4 1.9 + - - +
76C A 5.3 5.5 + - - -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 4.0 13.7 - - + -
121A ALA* 2.9 23.7 + - + +
122A PRO 4.2 0.4 - - - +
123A ILE 3.2 0.8 - - - -
124A GLN* 1.3 76.3 - - - +
126A SER* 1.3 68.3 + - - +
128A TRP* 3.4 43.0 - - - +
129A ALA* 2.8 28.2 + - - +
204A ALA* 3.4 25.1 - - + +
205A GLU* 2.9 25.6 + - - +
206A LYS 2.9 27.3 + - - -
207A LEU* 3.4 20.0 - - - +
211A GLU* 2.9 39.0 + - - -
230A PHE* 4.6 0.6 - - - -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 3.2 26.6 - - - +
122A PRO 3.1 16.6 + - - -
123A ILE 2.6 18.5 + - - -
125A ARG* 1.3 79.3 - - - +
127A LEU* 1.3 68.6 + - - +
129A ALA 3.2 3.3 + - - -
131A ASP* 3.1 36.7 + - - +
133A GLU 4.5 0.4 - - - -
134A THR* 3.5 21.5 + - - -
158A ILE* 3.6 10.0 - - - +
167A LEU* 4.3 1.4 - - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE 4.1 1.6 - - - +
124A GLN* 3.3 7.9 + - - +
126A SER* 1.3 82.5 + - - +
128A TRP* 1.3 61.9 + - - +
130A GLY* 3.4 9.4 + - - +
131A ASP 4.9 2.0 - - - +
158A ILE* 3.9 20.2 - - + -
162A ASP* 3.4 13.2 - - + +
163A THR* 3.0 35.2 - - - +
164A SER* 4.0 6.3 - - - +
167A LEU* 3.6 22.7 - - + -
225A ARG* 3.6 11.6 - - + +
228A ARG* 3.7 35.9 - - + +
229A ALA* 4.2 10.3 - - + +
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Residues in contact with TRP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A TRP* 4.9 7.0 - + - -
124A GLN 2.8 22.5 + - - +
125A ARG* 3.4 47.3 - - + +
127A LEU* 1.3 74.0 - - - +
129A ALA* 1.3 82.9 + - + +
130A GLY 3.1 1.4 + - - -
207A LEU* 6.2 0.2 - - + -
211A GLU* 3.8 9.0 + - - +
218A LEU* 6.2 0.2 - - - +
222A GLN* 3.3 34.7 + - - -
225A ARG* 3.2 20.8 - - - +
226A CYS* 3.7 23.6 - - - -
229A ALA* 3.6 13.2 - - + -
230A PHE* 3.8 27.4 - + + -
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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