Contacts of the helix formed by residues 526 - 533 (chain B) in PDB entry 2XI4
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 GLN 526 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A TRP* 6.1 0.5 - - - -
522B VAL* 2.9 41.2 + - + +
525B ASN* 1.3 85.6 - - + +
527B PHE* 1.3 64.1 + - + +
528B LEU 3.6 0.7 - - - -
529B PRO* 3.6 6.5 - - - +
530B LYS* 3.4 20.3 + - - +
1005B PEG 5.2 11.1 + - - +
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Residues in contact with PHE 527 (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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366A LEU* 3.8 20.4 - - + -
369A ASP* 4.2 18.6 - - + -
370A ALA* 3.6 41.5 - - + -
373A LEU* 3.8 24.5 - - + -
527A PHE* 4.4 6.1 - + - -
531A LEU* 4.1 7.4 - - + -
370B ALA* 4.3 11.0 - - + -
522B VAL* 3.1 6.7 + - + +
523B PHE* 3.9 21.8 - + - +
526B GLN* 1.3 77.5 - - + +
528B LEU* 1.3 71.7 + - - +
529B PRO 3.3 0.2 - - - -
530B LYS* 3.4 6.7 + - + +
531B LEU* 3.0 48.8 + - + +
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Residues in contact with LEU 528 (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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360B VAL* 4.4 9.4 - - + -
362B HIS* 5.4 1.8 - - - +
367B GLY* 3.9 34.5 - - - +
370B ALA* 4.6 4.3 - - + -
371B VAL* 4.1 8.1 - - + -
398B HIS* 5.5 0.7 - - + +
523B PHE* 2.7 39.1 + - + +
524B TRP* 3.4 37.9 - - + +
527B PHE* 1.3 76.9 - - - +
529B PRO* 1.4 61.9 - - + +
531B LEU* 2.9 11.7 + - + +
532B LEU* 2.9 46.0 + - + +
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Residues in contact with PRO 529 (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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524B TRP 3.3 24.2 - - - +
525B ASN* 4.0 12.1 - - - +
526B GLN 3.6 12.3 - - - +
527B PHE 3.5 3.1 - - - -
528B LEU* 1.4 89.3 - - + +
530B LYS* 1.3 54.9 + - - +
532B LEU* 3.1 11.1 + - + +
533B ASN* 2.9 34.9 + - - +
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Residues in contact with LYS 530 (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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365A ASP* 4.1 18.9 + - - +
366A LEU* 3.7 25.5 - - + +
369A ASP* 2.9 33.7 + - + +
526B GLN 3.4 18.1 + - - +
527B PHE* 3.4 5.6 + - + +
528B LEU 3.3 0.2 - - - -
529B PRO* 1.3 80.0 - - - +
531B LEU* 1.3 61.0 + - - +
533B ASN* 3.5 20.3 + - - +
534B ALA* 3.9 6.2 - - - +
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Residues in contact with LEU 531 (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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366A LEU* 3.8 19.2 - - + +
527A PHE* 4.0 10.8 - - + -
531A LEU* 4.4 2.0 - - + -
364B ASN* 4.1 7.2 + - - +
366B LEU* 3.7 25.9 - - + +
367B GLY* 3.6 28.7 - - - +
370B ALA* 3.9 19.1 - - + -
527B PHE* 3.0 38.3 + - + +
528B LEU* 2.9 12.0 + - + +
530B LYS* 1.3 74.1 - - - +
532B LEU* 1.3 73.5 + - + +
533B ASN 3.1 1.6 - - - -
534B ALA* 3.2 17.5 - - - +
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Residues in contact with LEU 532 (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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362B HIS* 3.8 32.8 - - + +
363B ALA* 3.9 25.4 - - + -
364B ASN* 3.6 35.2 + - - +
367B GLY* 3.9 11.0 - - - -
528B LEU* 2.9 41.8 + - + +
529B PRO* 3.1 8.0 + - + +
531B LEU* 1.3 74.7 - - + +
533B ASN* 1.3 56.7 + - - +
534B ALA 3.2 4.8 + - - -
535B THR 4.8 2.1 + - - -
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Residues in contact with ASN 533 (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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529B PRO 2.9 19.3 + - - +
530B LYS* 3.8 10.0 + - - +
531B LEU 3.1 0.6 - - - -
532B LEU* 1.3 75.9 - - - +
534B ALA* 1.3 56.7 + - - +
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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