Contacts of the helix formed by residues 460 - 469 (chain C) in PDB entry 2AXT
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 ASP 460 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455C PHE* 6.0 0.6 - - - +
458C GLY 3.6 3.6 + - - -
459C ILE* 1.3 71.8 - - - +
461C ARG* 1.3 70.8 + - - +
462C GLU* 3.1 25.0 + - - +
463C SER* 2.7 45.4 + - - +
464C GLU* 3.3 2.1 + - - -
465C PRO* 5.5 0.4 - - - +
224D GLN* 5.2 10.2 + - - +
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Residues in contact with ARG 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C ILE 3.0 8.8 + - - -
460C ASP* 1.3 73.7 + - - +
462C GLU* 1.3 62.5 + - - +
463C SER 3.2 0.5 + - - -
464C GLU* 3.8 13.3 + - - +
467C LEU* 5.1 3.3 - - - +
223D PHE* 3.1 47.3 - - + -
224D GLN 4.7 4.7 + - - +
225D ASP* 2.7 41.0 + - - +
241D GLU* 3.8 36.8 + - - +
242D GLU 2.8 28.1 + - - -
243D THR* 4.3 1.6 - - - +
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Residues in contact with GLU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C ASP* 3.1 12.6 + - - +
461C ARG* 1.3 79.1 - - - +
463C SER* 1.3 59.8 + - - +
464C GLU 4.0 0.6 + - - -
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Residues in contact with SER 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C ASP* 2.7 35.0 + - - +
462C GLU* 1.3 77.9 - - - +
464C GLU* 1.3 59.1 + - - +
465C PRO* 3.0 16.3 - - - +
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Residues in contact with GLU 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C ILE* 3.3 23.1 - - + -
460C ASP 3.3 5.4 + - - +
461C ARG 3.8 5.7 + - - +
462C GLU 4.0 0.4 + - - -
463C SER* 1.3 70.8 - - - +
465C PRO* 1.3 70.6 - - + +
466C VAL* 3.1 2.3 - - - +
467C LEU* 2.7 62.6 + - + +
468C SER* 3.6 4.0 + - - -
223D PHE* 3.6 27.5 - - + -
245D SER* 3.1 13.3 - - - -
247D VAL* 4.5 7.4 - - - +
248D THR* 2.5 30.3 + - - +
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Residues in contact with PRO 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU 4.0 13.2 - - - +
138A GLY* 4.7 2.9 - - - -
459C ILE* 4.0 16.2 - - + -
460C ASP* 5.5 0.9 - - + +
463C SER 3.0 12.0 - - - +
464C GLU* 1.3 81.9 - - + +
466C VAL* 1.3 62.2 + - + +
468C SER* 2.8 25.7 + - - +
469C MET* 3.0 24.8 - - + +
32I PRO* 3.3 41.5 - - + -
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.3 19.3 - - + +
464C GLU* 2.9 4.9 + - + +
465C PRO* 1.3 74.3 - - + +
467C LEU* 1.3 58.4 + - - +
468C SER 2.9 6.6 + - - -
469C MET* 3.0 39.6 + - + +
247D VAL* 4.0 30.5 - - + +
248D THR* 3.4 39.0 - - + +
251D ARG* 4.0 22.7 + - + +
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Residues in contact with LEU 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ARG 5.1 3.8 - - - +
464C GLU* 2.7 59.6 + - + +
466C VAL* 1.3 71.5 - - - +
468C SER* 1.3 55.0 + - - -
469C MET 3.5 2.1 + - - +
247D VAL* 4.7 20.9 - - + -
29T ILE* 5.5 12.6 - - + -
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Residues in contact with SER 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C GLU 3.6 2.1 + - - -
465C PRO* 2.8 24.7 + - - +
466C VAL 2.9 0.2 + - - -
467C LEU* 1.3 78.6 - - - +
469C MET* 1.3 61.1 + - - +
470C PRO* 4.4 3.5 - - - +
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Residues in contact with MET 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 3.4 33.0 - - + -
25A ASP* 4.9 1.8 - - - +
136A ARG 4.5 1.6 - - - +
137A LEU* 3.7 25.8 - - + -
465C PRO* 3.0 23.3 - - + +
466C VAL* 3.0 45.2 + - + +
467C LEU 3.5 1.6 - - - +
468C SER* 1.3 81.2 - - - +
470C PRO* 1.3 72.6 - - + +
471C SER* 3.2 4.2 + - - -
251D ARG* 4.0 24.3 + - - +
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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