Contacts of the helix formed by residues 123 - 129 (chain B) in PDB entry 4FDI
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 LEU 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B LEU* 3.2 17.5 - - + +
88B THR* 3.5 29.6 - - + -
117B ILE* 4.0 19.5 - - + -
121B GLU* 4.5 4.3 - - + +
122B GLN* 1.3 76.5 - - - +
124B LEU* 1.3 66.5 + - - +
125B PRO* 3.4 7.9 - - + -
126B GLU* 2.7 28.1 + - - +
127B LEU* 3.1 11.6 + - - +
141B TRP* 3.6 31.4 - - + -
143B LEU* 4.2 9.0 - - + -
154B HIS* 3.6 34.1 - - + +
346B PHE* 4.3 1.3 - - - -
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Residues in contact with LEU 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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35B LEU* 4.2 7.9 - - + -
86B LEU* 5.1 6.1 - - + -
87B LEU* 2.9 16.6 + - + +
123B LEU* 1.3 69.5 - - - +
125B PRO* 1.4 66.9 - - + +
127B LEU* 3.0 6.2 + - - +
128B LEU* 2.9 47.7 + - + +
227B PHE* 3.8 25.8 - - + -
345B LEU 4.2 6.7 - - - +
346B PHE* 3.6 41.2 - - + +
349B SER* 3.7 27.8 - - - +
350B LEU* 3.9 12.8 - - + -
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Residues in contact with PRO 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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87B LEU* 4.4 8.1 - - + -
123B LEU* 3.5 7.6 - - + -
124B LEU* 1.4 95.8 - - + +
126B GLU* 1.3 61.8 + - - +
128B LEU* 4.0 6.0 - - + +
129B LYS* 3.3 19.8 + - - +
135B SER* 3.7 26.0 + - - +
154B HIS 3.7 14.8 - - - +
155B GLY 3.5 23.1 - - - +
156B PHE* 3.7 24.2 - - + +
227B PHE* 4.0 14.8 - - + -
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Residues in contact with GLU 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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119B ASP 5.7 0.7 - - - +
121B GLU 3.5 8.1 - - - +
122B GLN* 3.4 11.4 - - + +
123B LEU* 2.7 36.0 + - - +
125B PRO* 1.3 77.3 - - - +
127B LEU* 1.3 66.0 + - + +
129B LYS* 3.4 21.0 - - - +
130B LYS* 4.5 2.9 + - - -
153B LYS 4.0 5.2 - - - +
154B HIS* 3.2 44.4 + - - +
155B GLY* 3.5 7.1 + - - +
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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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122B GLN* 3.7 37.9 - - + +
123B LEU 3.1 6.3 + - - +
124B LEU 3.0 6.3 + - - +
126B GLU* 1.3 80.7 - - + +
128B LEU* 1.3 62.8 + - - +
129B LYS 3.2 2.5 + - - -
130B LYS* 3.1 36.0 + - - +
346B PHE* 3.6 35.9 - - + -
350B LEU* 3.8 18.4 - - + -
355B LEU* 3.3 14.1 - - + +
356B THR 5.7 1.8 - - - +
358B PRO* 4.0 19.1 - - + -
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Residues in contact with LEU 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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33B ILE* 4.1 15.3 - - + -
124B LEU* 2.9 35.9 + - + +
125B PRO* 4.0 5.6 - - + +
126B GLU 3.4 0.2 - - - -
127B LEU* 1.3 74.5 - - - +
129B LYS* 1.3 59.2 + - - +
131B ALA* 2.9 19.7 + - - -
132B GLY 3.6 0.7 + - - -
133B TYR* 3.3 31.8 + - + -
135B SER* 4.9 0.4 - - - +
227B PHE* 3.8 37.9 - - + -
349B SER 4.0 13.5 - - - +
350B LEU* 4.0 13.7 - - + -
353B ALA* 3.8 27.4 - - + -
355B LEU* 4.2 2.0 - - - -
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Residues in contact with LYS 129 (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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125B PRO 3.3 10.8 + - - +
126B GLU* 3.4 17.3 - - - +
127B LEU 3.2 0.6 - - - -
128B LEU* 1.3 77.2 - - - +
130B LYS* 1.3 61.9 + - - +
132B GLY* 2.9 16.5 + - - -
133B TYR* 4.1 16.6 + - - +
155B GLY* 5.2 9.1 + - - +
157B ASP* 3.1 29.2 + - - +
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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