Contacts of the helix formed by residues 515 - 526 (chain B) in PDB entry 2AX1
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 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511B LEU 3.7 1.4 + - - -
512B LEU 3.0 11.0 + - - -
513B SER 3.2 2.2 + - - -
514B ARG* 1.3 84.1 - - - +
516B GLY* 1.3 63.7 + - - -
518B ALA* 3.4 7.3 + - - +
519B ALA* 2.9 32.0 + - - -
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Residues in contact with GLY 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B GLY* 1.3 70.8 - - - -
517B ARG* 1.3 63.4 + - - -
519B ALA* 3.1 12.2 + - - +
520B ILE* 3.2 18.0 + - - +
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B GLU* 3.8 18.4 + - - +
455B GLU* 3.8 20.6 + - - +
457B LEU* 3.6 50.9 - - + +
458B ASP* 5.1 11.5 + - - -
516B GLY* 1.3 70.3 - - - -
518B ALA* 1.3 62.6 + - - +
520B ILE* 3.1 27.1 + - + +
521B CYS* 3.2 15.9 + - - -
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B LEU* 4.2 14.8 - - + -
440B GLU* 5.9 1.6 - - - +
457B LEU* 3.8 14.3 - - + +
511B LEU* 3.5 31.7 - - + +
514B ARG* 3.9 14.1 - - + -
515B GLY 3.4 8.9 + - - +
516B GLY 3.1 0.4 - - - -
517B ARG* 1.3 79.2 - - - +
519B ALA* 1.3 61.3 + - - +
521B CYS* 3.1 15.5 + - - +
522B GLY 3.1 9.5 + - - -
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LEU 3.3 13.0 + - - +
512B LEU* 3.7 20.5 - - + +
515B GLY* 2.9 35.2 + - - +
516B GLY 3.1 3.8 + - - +
518B ALA* 1.3 76.1 - - - +
520B ILE* 1.3 58.3 + - + +
522B GLY 3.2 0.7 + - - -
523B LYS* 3.0 28.8 + - - +
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B PRO* 4.1 19.5 - - + +
461B GLN* 5.4 2.0 - - - +
516B GLY 3.2 14.5 + - - +
517B ARG* 3.1 19.8 + - + +
519B ALA* 1.3 77.1 - - + +
521B CYS* 1.3 62.0 + - - +
523B LYS* 3.4 6.7 + - + -
524B TYR* 3.1 46.0 + - + +
539B ILE* 4.2 14.8 - - + -
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Residues in contact with CYS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PHE* 3.9 22.9 - - + -
457B LEU* 4.0 21.1 - - - -
460B PRO* 3.7 33.0 - - - -
511B LEU* 4.0 12.6 - - + -
517B ARG 3.2 15.4 + - - -
518B ALA* 3.1 10.2 + - - +
520B ILE* 1.3 74.3 - - - +
522B GLY* 1.3 65.3 - - - +
525B LEU* 3.0 38.7 + - + +
526B PHE* 3.7 0.7 - - - -
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Residues in contact with GLY 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ARG* 3.4 30.1 + - - +
511B LEU* 3.6 25.2 - - - +
512B LEU* 4.6 2.9 - - - -
518B ALA 3.1 10.5 + - - -
519B ALA 3.2 3.5 + - - -
521B CYS* 1.3 76.4 - - - +
523B LYS* 1.3 63.3 + - - +
526B PHE* 3.3 18.7 + - - +
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ARG* 4.9 2.8 + - - +
512B LEU* 4.3 8.0 - - + +
519B ALA 3.0 16.6 + - - +
520B ILE* 3.6 8.3 - - + +
521B CYS 3.2 0.2 - - - -
522B GLY* 1.3 80.9 - - - +
524B TYR* 1.3 85.9 + - + +
527B ASN* 3.3 26.3 + - - +
534B LEU* 3.9 30.9 - - + +
535B LYS 3.5 24.8 + - - -
536B LEU* 3.7 16.2 - - + -
537B THR* 4.8 4.8 + - - -
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Residues in contact with TYR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B PRO* 4.7 6.5 - - + -
469B LEU* 4.2 4.7 - - + -
472B PHE* 3.5 54.9 - + + +
520B ILE* 3.1 35.4 + - + +
523B LYS* 1.3 111.7 + - + +
525B LEU* 1.3 65.9 + - - +
526B PHE 3.5 0.3 + - - -
527B ASN* 3.8 6.9 + - - +
528B TRP* 5.5 0.2 - - - -
536B LEU* 3.9 22.4 - - + -
537B THR* 2.6 42.0 + - - -
538B PRO 4.6 1.0 + - - -
539B ILE* 3.6 27.7 - - + +
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ARG* 5.2 1.2 + - - -
426B MET* 4.1 24.2 - - + +
430B PHE* 3.5 38.4 - - + -
459B LEU* 4.4 9.4 - - + -
460B PRO* 4.3 11.2 - - + -
463B ILE* 3.9 19.3 - - + -
472B PHE* 3.7 26.2 - - + -
521B CYS* 3.0 34.1 + - + +
524B TYR* 1.3 75.5 - - - +
526B PHE* 1.3 69.5 + - + +
527B ASN 3.6 0.2 - - - -
528B TRP* 2.9 23.8 + - - -
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Residues in contact with PHE 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B ARG 4.6 0.2 - - - -
426B MET* 3.5 32.1 - - + -
427B THR* 3.4 30.1 - - - -
430B PHE* 4.2 13.0 - + + -
504B ALA* 3.8 24.7 - - + +
507B VAL* 4.3 5.4 - - + -
508B ARG* 3.6 28.4 + - + -
511B LEU* 3.7 22.4 - - + -
521B CYS 3.7 9.4 - - - -
522B GLY* 3.3 22.0 + - - +
524B TYR 3.3 0.2 - - - -
525B LEU* 1.3 88.8 - - + +
527B ASN* 1.3 61.1 + - - +
528B TRP* 3.0 19.1 - + - +
529B ALA* 3.0 18.4 + - + +
530B VAL 4.1 0.9 + - - -
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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