Contacts of the helix formed by residues 122 - 127 (chain A) in PDB entry 4FE1
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 GLY 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ILE 2.6 9.7 + - - +
121A VAL* 1.3 73.7 - - - +
123A GLN* 1.3 54.5 + - - -
124A GLY* 3.0 12.6 + - - -
125A ILE* 3.4 11.8 + - - +
449B PHE* 3.6 28.6 - - - +
451B THR* 5.4 7.9 - - - -
454B LYS* 5.2 0.7 - - - -
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Residues in contact with GLN 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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117A VAL* 3.3 24.2 - - + +
118A TRP* 3.1 40.9 + - - +
120A ILE* 2.9 31.5 + - - +
121A VAL* 3.5 9.2 - - + +
122A GLY* 1.3 75.7 - - - +
124A GLY* 1.3 62.8 + - - +
125A ILE* 3.1 1.3 - - - -
126A LEU* 3.0 23.2 + - + +
449B PHE* 3.5 31.2 - - + -
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Residues in contact with GLY 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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117A VAL* 3.9 10.1 - - - -
118A TRP 4.0 6.2 + - - -
119A PRO* 4.5 11.0 - - - -
120A ILE 4.3 2.6 + - - +
122A GLY 3.0 3.8 + - - -
123A GLN* 1.3 81.3 - - - +
125A ILE* 1.3 57.3 + - - +
126A LEU 2.9 6.4 + - - -
127A ASN* 3.1 26.0 + - - +
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Residues in contact with ILE 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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122A GLY 3.4 10.7 + - - +
123A GLN 4.0 1.3 - - - +
124A GLY* 1.3 75.1 - - - +
126A LEU* 1.3 64.8 + - + +
127A ASN 3.2 4.3 + - - +
128A GLY* 4.6 0.5 - - - -
666A GLY* 3.7 10.5 - - - +
667A SER* 3.7 35.0 - - - +
668A ALA* 3.4 13.7 - - - +
670A SER* 4.2 8.1 - - - +
448B ALA 4.3 0.7 - - - +
449B PHE* 3.6 52.7 - - + +
450B GLY* 4.5 2.7 - - - +
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Residues in contact with LEU 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 VAL* 3.9 22.2 - - + -
123A GLN* 3.4 17.3 - - + +
124A GLY 2.9 1.8 + - - -
125A ILE* 1.3 81.9 - - + +
127A ASN* 1.3 58.9 + - - +
128A GLY 2.9 8.1 + - - -
136A GLY 3.7 6.8 - - - +
137A ILE* 3.8 20.3 - - + +
668A ALA* 3.2 29.3 - - - +
670A SER* 3.6 21.1 - - - +
671A ALA* 3.5 33.2 - - + +
449B PHE* 4.4 14.8 - - + -
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Residues in contact with ASN 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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116A VAL* 3.5 9.7 - - - +
117A VAL* 2.8 53.7 + - - +
119A PRO* 5.6 2.6 - - - +
124A GLY* 3.1 20.6 + - - +
125A ILE 4.1 3.1 - - - +
126A LEU* 1.3 74.7 - - - +
128A GLY* 1.3 63.6 + - - +
135A HIS* 3.3 28.0 - - + -
136A GLY* 3.5 27.9 - - - +
137A ILE 4.4 0.3 + - - -
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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