Contacts of the helix formed by residues 488 - 501 (chain A) in PDB entry 2XFN
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 SER 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A LEU* 4.5 2.9 - - - -
117A ASN* 3.4 41.7 - - - -
120A ARG* 3.9 4.2 - - - +
486A LEU 3.8 0.8 + - - -
487A PRO* 1.3 77.8 - - - +
489A VAL* 1.3 59.6 + - - +
490A PRO* 3.5 13.3 - - - +
491A GLY* 2.9 20.4 + - - -
492A LEU* 2.8 26.3 + - - +
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Residues in contact with VAL 489 (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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110A ILE* 3.7 42.8 - - + +
113A LEU* 4.3 6.2 + - + +
114A ASP* 3.9 24.7 + - + +
157A TRP* 3.8 34.1 - - + -
488A SER* 1.3 72.1 - - - +
490A PRO* 1.4 71.7 - - + +
492A LEU* 3.1 10.2 + - + +
493A LEU* 2.9 31.5 + - + +
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Residues in contact with PRO 490 (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 ASN* 5.8 0.2 - - - +
157A TRP* 3.4 48.7 - - + +
488A SER* 3.5 14.1 - - - +
489A VAL* 1.4 92.7 - - + +
491A GLY* 1.3 54.8 + - - +
493A LEU* 3.6 12.8 - - + +
494A ARG* 2.9 36.1 + - + +
1502A C15 4.9 4.7 - - - +
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Residues in contact with GLY 491 (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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487A PRO* 4.0 11.7 - - - -
488A SER* 2.9 20.6 + - - -
490A PRO* 1.3 77.4 - - - +
492A LEU* 1.3 55.8 + - - +
494A ARG* 3.3 9.7 + - - +
495A LEU* 3.0 30.4 + - - +
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Residues in contact with LEU 492 (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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110A ILE* 3.7 30.3 - - + -
113A LEU* 3.8 17.0 - - + -
487A PRO* 3.8 18.3 - - + +
488A SER 2.8 13.2 + - - +
489A VAL* 3.1 11.2 + - + +
491A GLY* 1.3 73.9 - - - +
493A LEU* 1.3 62.0 + - + +
495A LEU* 3.2 15.0 + - + +
496A ILE* 2.9 53.5 + - + +
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Residues in contact with LEU 493 (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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157A TRP* 3.7 36.1 - - + -
489A VAL* 2.9 25.1 + - + +
490A PRO* 3.6 8.1 - - + +
492A LEU* 1.3 78.8 - - + +
494A ARG* 1.3 57.7 + - - +
496A ILE* 3.3 20.4 + - + +
497A GLY* 2.9 26.0 + - - -
1502A C15 6.5 0.4 - - + -
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Residues in contact with ARG 494 (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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490A PRO* 2.9 20.8 + - + +
491A GLY* 3.5 8.5 - - - +
493A LEU* 1.3 74.5 - - + +
495A LEU* 1.3 66.1 + - + +
497A GLY* 3.4 2.2 + - - +
498A LEU* 3.0 33.8 + - + +
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Residues in contact with LEU 495 (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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487A PRO* 4.3 24.2 - - + -
491A GLY 3.0 18.4 + - - +
492A LEU* 3.4 18.2 - - + +
494A ARG* 1.3 76.2 - - + +
496A ILE* 1.3 56.0 + - + +
498A LEU* 3.3 16.2 + - + +
499A THR* 3.0 32.3 + - - -
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Residues in contact with ILE 496 (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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492A LEU* 2.9 46.1 + - + +
493A LEU* 3.6 22.9 - - + +
494A ARG 3.3 0.2 - - - -
495A LEU* 1.3 70.4 - - + +
497A GLY* 1.3 67.3 + - - +
499A THR* 3.4 7.6 + - - -
500A THR* 2.9 32.7 + - - +
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Residues in contact with GLY 497 (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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493A LEU 2.9 19.2 + - - -
494A ARG* 3.4 2.4 + - - -
496A ILE* 1.3 72.3 - - - +
498A LEU* 1.3 58.7 + - - +
500A THR* 3.2 10.7 + - - -
501A ILE* 3.0 35.4 + - - +
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Residues in contact with LEU 498 (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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494A ARG* 3.0 26.3 + - + +
495A LEU* 3.7 16.6 - - + +
496A ILE 3.2 0.2 - - - -
497A GLY* 1.3 73.6 - - - +
499A THR* 1.3 63.1 + - - +
501A ILE* 3.0 34.9 + - + +
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Residues in contact with THR 499 (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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495A LEU* 3.0 18.5 + - - +
496A ILE* 3.4 6.7 + - - -
498A LEU* 1.3 75.6 - - - +
500A THR* 1.3 60.3 + - - +
501A ILE 4.0 4.7 - - - +
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Residues in contact with THR 500 (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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496A ILE* 2.9 21.0 + - - +
497A GLY* 3.4 12.1 - - - -
498A LEU 3.2 0.4 - - - -
499A THR* 1.3 78.3 - - - +
501A ILE* 1.3 61.3 + - + +
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Residues in contact with ILE 501 (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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497A GLY* 3.0 21.1 + - - +
498A LEU* 3.0 29.1 + - + +
499A THR 4.0 4.0 - - - +
500A THR* 1.3 86.9 - - + +
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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