Contacts of the helix formed by residues 123 - 129 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.2 20.0 - - + +
88A THR* 3.4 30.5 - - + -
117A ILE* 4.0 17.7 - - + -
121A GLU* 4.8 2.9 - - + +
122A GLN* 1.3 75.9 - - - +
124A LEU* 1.3 67.0 + - - +
125A PRO* 3.4 8.1 - - + -
126A GLU* 2.7 27.4 + - - +
127A LEU* 3.1 12.3 + - - +
141A TRP* 3.6 33.0 - - + -
143A LEU* 4.2 7.6 - - + -
154A HIS* 3.6 35.2 - - + +
346A PHE* 4.3 1.1 - - - -
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Residues in contact with LEU 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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35A LEU* 4.2 8.5 - - + -
86A LEU* 5.1 6.1 - - + -
87A LEU* 2.9 16.0 + - + +
123A LEU* 1.3 70.6 - - - +
125A PRO* 1.4 66.1 - - + +
127A LEU* 3.2 4.5 + - - +
128A LEU* 2.9 42.6 + - + +
227A PHE* 3.7 26.5 - - + -
345A LEU 4.4 4.5 - - - +
346A PHE* 3.7 41.9 - - + +
349A SER* 3.7 29.4 - - - +
350A LEU* 3.7 18.4 - - + -
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Residues in contact with PRO 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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87A LEU* 4.3 9.2 - - + -
123A LEU* 3.5 7.9 - - + -
124A LEU* 1.4 95.6 - - + +
126A GLU* 1.3 62.1 + - - +
128A LEU* 3.6 10.5 + - + +
129A LYS* 3.7 12.0 + - - +
133A TYR 5.5 0.5 - - - +
135A SER* 3.6 27.7 + - - +
154A HIS 3.6 15.0 - - - +
155A GLY 3.6 22.2 - - - +
156A PHE* 3.6 27.6 - - + +
227A PHE* 4.1 12.1 - - + -
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Residues in contact with GLU 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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119A ASP 5.7 0.3 - - - +
121A GLU 3.5 14.3 - - - +
122A GLN* 3.6 3.6 - - + -
123A LEU* 2.7 37.4 + - - +
125A PRO* 1.3 78.4 - - - +
127A LEU* 1.3 63.8 + - + +
129A LYS* 3.0 31.9 - - - +
130A LYS* 4.5 1.7 + - - +
153A LYS 4.3 4.3 - - - +
154A HIS* 3.1 45.6 + - - +
155A GLY* 3.5 8.0 + - - +
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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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122A GLN* 3.5 31.9 - - + +
123A LEU 3.1 9.0 + - - +
124A LEU 3.2 2.7 + - - +
126A GLU* 1.3 82.8 - - + +
128A LEU* 1.3 58.0 + - - +
130A LYS* 3.0 49.0 + - + +
346A PHE* 3.5 36.6 - - + -
350A LEU* 3.8 24.0 - - + -
355A LEU* 3.2 13.7 - - - +
356A THR 5.5 1.6 - - - +
357A PRO* 5.5 0.2 - - + -
358A PRO* 4.1 14.4 - - + -
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Residues in contact with LEU 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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33A ILE* 4.3 9.9 - - + -
124A LEU* 2.9 37.0 + - + +
125A PRO* 4.0 5.6 - - + +
126A GLU 3.3 0.6 - - - -
127A LEU* 1.3 71.2 - - - +
129A LYS* 1.3 56.1 + - - +
130A LYS 3.0 5.2 - - - -
131A ALA* 2.9 18.0 + - - +
133A TYR* 3.3 35.4 + - + -
135A SER* 4.8 0.4 - - - +
227A PHE* 3.6 42.4 - - + -
349A SER 3.9 11.4 - - - +
350A LEU* 4.1 11.9 - - + -
353A ALA* 3.6 29.2 - - + -
355A LEU* 4.0 2.5 - - - -
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Residues in contact with LYS 129 (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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125A PRO 3.7 10.4 + - - -
126A GLU* 3.0 25.3 + - - +
128A LEU* 1.3 76.7 - - - +
130A LYS* 1.3 58.8 + - + +
131A ALA 3.1 2.2 - - - -
132A GLY* 3.2 14.4 + - - -
133A TYR* 3.9 20.3 - - - +
155A GLY* 3.3 32.4 + - - -
156A PHE 5.3 0.8 + - - -
157A ASP* 3.9 20.7 + - - -
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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