Contacts of the helix formed by residues 448 - 458 (chain A) in PDB entry 2XJF
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 THR 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.6 41.1 - - + -
112A VAL 3.6 7.4 - - - +
113A ASP* 4.1 1.1 - - - -
114A ALA 4.3 0.8 + - - -
119A LEU* 4.1 7.0 - - + -
440A LEU 2.7 26.2 + - - +
441A PHE 3.1 10.4 + - - -
442A ARG* 3.7 12.3 - - - +
447A GLN* 1.3 76.8 - - - +
449A LEU* 1.3 66.9 + - - +
450A PHE* 3.5 5.1 + - - -
451A ALA* 3.1 15.8 + - - +
452A SER* 3.0 21.8 + - - -
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Residues in contact with LEU 449 (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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99A GLY 5.5 4.3 - - - +
101A VAL* 5.4 0.7 - - + -
112A VAL* 3.1 22.6 + - + +
113A ASP 3.6 16.5 - - - +
114A ALA* 3.9 10.3 - - + -
144A ARG* 3.4 54.5 - - - +
152A ILE* 3.9 28.7 - - + -
154A ASN* 5.8 0.2 - - - +
448A THR* 1.3 70.8 - - - +
450A PHE* 1.3 64.3 + - - +
452A SER* 2.8 23.9 + - - +
453A GLN* 2.9 37.5 + - + +
1489A DG2 5.1 0.9 - - - +
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Residues in contact with PHE 450 (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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98A ARG* 3.7 38.6 - - - +
99A GLY* 4.9 11.7 - - - -
154A ASN* 4.1 19.5 - - - +
351A ASP 5.8 0.7 - - - -
353A ILE* 3.8 26.7 - - + -
370A LEU* 4.7 5.8 - - + -
372A ILE* 4.5 5.2 - - + -
440A LEU* 3.6 43.7 - - + +
441A PHE* 4.2 8.5 - + - -
448A THR* 3.1 10.7 + - - +
449A LEU* 1.3 79.1 - - - +
451A ALA* 1.3 57.8 + - - +
453A GLN* 3.2 11.1 + - - +
454A VAL* 3.0 55.4 + - + +
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Residues in contact with ALA 451 (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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440A LEU 4.5 0.2 + - - -
441A PHE* 3.3 48.0 - - + +
447A GLN* 4.2 16.4 - - + +
448A THR* 3.1 12.2 + - - +
450A PHE* 1.3 79.5 - - - +
452A SER* 1.3 55.6 + - - +
454A VAL* 3.4 5.6 + - - +
455A MET* 3.1 34.6 + - + +
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Residues in contact with SER 452 (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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114A ALA* 3.1 34.2 - - - +
447A GLN* 5.4 5.7 - - - +
448A THR 3.0 9.7 + - - -
449A LEU* 2.8 20.4 + - - +
451A ALA* 1.3 74.5 - - - +
453A GLN* 1.3 63.8 + - - +
455A MET* 4.1 8.8 - - - +
456A ARG* 3.1 39.3 + - - +
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Residues in contact with GLN 453 (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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144A ARG* 4.9 5.1 - - - +
152A ILE* 6.1 0.4 - - - +
154A ASN* 4.3 19.0 + - - +
353A ILE* 3.7 34.8 - - + +
354A PHE* 5.8 5.3 - - - +
358A LEU* 5.0 11.6 - - + +
449A LEU* 2.9 44.7 + - + +
450A PHE* 3.6 17.8 - - - +
452A SER* 1.3 73.0 - - - +
454A VAL* 1.3 60.9 + - - +
457A TYR* 3.0 49.7 + - + +
1489A DG2 5.8 2.8 + - - +
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Residues in contact with VAL 454 (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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38A ASN* 3.3 6.5 - - - +
353A ILE* 4.2 8.5 - - + -
370A LEU* 3.6 18.2 - - + -
372A ILE* 4.1 7.0 - - + -
441A PHE* 4.7 4.9 - - + -
450A PHE* 3.0 46.7 + - + +
451A ALA* 3.6 9.6 - - - +
453A GLN* 1.3 75.9 - - - +
455A MET* 1.3 65.0 + - + +
458A ALA* 3.0 28.1 + - + -
461A TYR* 3.9 36.3 - - + -
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Residues in contact with MET 455 (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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38A ASN* 3.5 29.7 - - - +
39A ARG* 2.7 29.5 + - - -
447A GLN* 3.6 33.2 - - - +
451A ALA* 3.1 21.0 + - + +
452A SER* 4.1 7.2 - - - +
453A GLN 3.4 0.2 - - - -
454A VAL* 1.3 78.4 - - + +
456A ARG* 1.3 51.2 + - - +
461A TYR* 6.2 1.1 - - + -
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Residues in contact with ARG 456 (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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39A ARG* 3.4 17.2 + - - +
114A ALA* 5.6 4.2 - - - +
115A TYR* 5.4 5.9 + - - -
361A LYS* 5.3 2.1 - - - +
452A SER* 3.1 32.1 + - - +
455A MET* 1.3 79.4 - - - +
457A TYR* 1.3 97.2 + - + +
1489A DG2 5.2 5.6 - - - -
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Residues in contact with TYR 457 (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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39A ARG* 3.6 3.8 + - - +
353A ILE* 4.5 2.7 - - + -
357A ILE* 3.4 13.7 - - + +
358A LEU* 3.6 42.2 - - + +
361A LYS* 4.0 21.1 - - + +
362A LYS* 3.6 35.8 + - + -
368A THR* 2.8 25.6 + - - +
453A GLN* 3.0 30.9 + - + +
456A ARG* 1.3 109.0 - - + +
458A ALA* 1.3 54.5 + - - +
459A ASP 3.7 0.2 + - - -
1489A DG2 2.7 40.0 + - - -
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Residues in contact with ALA 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 2.8 26.5 - - - +
39A ARG* 3.2 7.6 + - - -
353A ILE* 4.7 0.2 - - + -
357A ILE* 4.0 6.2 - - + +
368A THR* 3.5 4.5 - - - -
370A LEU* 3.7 32.8 - - + -
453A GLN 4.2 0.6 + - - -
454A VAL* 3.0 25.8 + - + +
457A TYR* 1.3 75.7 - - - +
459A ASP* 1.3 61.2 + - - +
460A LEU 3.2 10.5 - - - +
461A TYR* 4.5 0.4 - - + -
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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