Contacts of the helix formed by residues 387 - 400 (chain B) in PDB entry 1XR2
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 GLU 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B LYS* 1.3 79.2 - - - +
388B TYR* 1.3 67.1 + - - +
389B THR* 3.4 11.0 - - + +
390B GLU* 3.2 8.7 + - + +
391B ARG* 3.1 16.0 + - - +
1203B SO4 4.1 11.2 - - - +
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Residues in contact with TYR 388 (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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387B GLU* 1.3 71.8 - - - +
389B THR* 1.3 61.4 + - + +
391B ARG* 2.9 13.4 + - - +
392B ASP* 2.7 59.3 + - + +
396B ARG* 4.7 0.9 + - - -
637B ASP* 3.6 40.4 - - + -
661B ILE* 3.4 40.4 + - + -
662B LYS* 3.7 27.5 - - + -
663B GLN* 2.8 39.1 + - - +
697B LEU* 4.8 0.7 - - - +
1203B SO4 3.1 25.7 + - - +
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU* 4.7 8.8 + - + +
388B TYR* 1.3 88.7 - - + +
390B GLU* 1.3 70.8 + - - +
392B ASP* 3.2 5.7 + - - +
393B ARG* 3.2 21.1 + - - +
661B ILE* 5.1 13.5 - - + -
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LYS* 4.0 25.1 - - + -
387B GLU* 3.2 11.8 + - + +
388B TYR 3.2 0.6 - - - -
389B THR* 1.3 84.4 + - - +
391B ARG* 1.3 62.6 + - - +
393B ARG* 3.5 5.4 + - - +
394B ILE* 3.3 28.9 + - + +
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Residues in contact with ARG 391 (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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384B ARG* 3.4 44.7 - - - +
386B LYS* 2.9 34.1 + - + +
387B GLU 3.1 14.0 + - - +
388B TYR* 2.9 20.7 + - - +
390B GLU* 1.3 75.4 - - - +
392B ASP* 1.3 64.1 + - - +
394B ILE* 3.2 9.3 + - - +
395B GLN* 2.9 33.1 + - - +
611B PRO* 3.8 23.8 - - + +
635B GLU 3.8 5.9 + - - -
636B PHE 3.5 10.7 + - - -
637B ASP* 2.8 31.3 + - - +
1203B SO4 2.8 39.0 + - - -
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Residues in contact with ASP 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B TYR* 2.7 43.8 + - + +
389B THR* 3.3 12.1 - - - +
391B ARG* 1.3 73.3 - - - +
393B ARG* 1.3 64.7 + - - +
395B GLN* 3.8 7.8 - - - +
396B ARG* 2.8 65.0 + - - +
614B GLN* 5.4 0.5 + - - -
663B GLN* 3.2 15.2 + - - -
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B THR 3.2 8.4 + - - +
390B GLU* 3.8 10.1 - - - +
392B ASP* 1.3 78.5 - - - +
394B ILE* 1.3 66.1 + - + +
396B ARG* 3.6 7.0 - - - +
397B GLU* 3.2 23.9 + - - +
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Residues in contact with ILE 394 (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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386B LYS* 3.8 26.7 - - + +
390B GLU* 3.3 16.6 - - + +
391B ARG* 3.2 7.5 + - - +
393B ARG* 1.3 74.8 - - + +
395B GLN* 1.3 66.3 + - - +
397B GLU* 3.4 6.7 + - - +
398B ARG* 3.0 24.1 + - + +
611B PRO* 4.4 16.6 - - + -
612B GLU* 3.9 31.6 - - + -
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Residues in contact with GLN 395 (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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384B ARG* 3.9 2.2 - - - +
388B TYR* 5.6 0.2 - - - -
391B ARG* 2.9 27.5 + - - +
392B ASP* 3.8 7.5 - - - +
394B ILE* 1.3 69.9 - - - +
396B ARG* 1.3 67.8 + - - +
398B ARG* 2.8 5.7 + - - -
399B LEU* 2.7 41.2 + - + +
611B PRO 3.0 25.4 + - - +
612B GLU 3.9 12.8 - - - +
613B THR 3.1 9.1 + - - -
614B GLN* 3.2 37.5 + - + +
637B ASP* 2.9 35.1 + - - +
663B GLN* 5.1 1.0 + - - -
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Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B TYR* 4.7 0.8 + - - -
392B ASP* 2.8 57.1 + - - +
393B ARG* 3.6 6.7 - - - +
395B GLN* 1.3 72.1 - - + +
397B GLU* 1.3 56.7 + - - +
399B LEU* 5.0 2.7 - - - -
400B ASN* 3.0 30.3 + - - -
401B LEU 4.6 1.4 + - - -
402B PRO 6.0 0.4 + - - -
614B GLN* 5.4 3.8 - - - +
663B GLN* 3.6 29.4 + - - +
696B GLU* 2.8 43.6 + - - +
697B LEU* 4.7 4.6 - - - +
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Residues in contact with GLU 397 (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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393B ARG 3.2 14.4 + - - +
394B ILE* 3.7 5.6 - - - +
396B ARG* 1.3 80.1 - - - +
398B ARG* 1.3 61.0 + - - +
400B ASN* 3.3 24.2 + - - +
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Residues in contact with ARG 398 (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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394B ILE* 3.0 16.3 + - + +
395B GLN* 2.8 12.0 + - - +
397B GLU* 1.3 79.5 - - - +
399B LEU* 1.3 66.5 + - + +
400B ASN* 4.2 5.2 - - - +
570B GLY* 4.9 8.9 + - - -
571B ILE 4.4 3.0 + - - -
572B LYS* 3.7 36.5 - - - +
612B GLU* 2.8 58.5 + - + +
613B THR* 4.0 4.6 + - - +
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Residues in contact with LEU 399 (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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395B GLN* 2.7 47.7 + - + +
396B ARG* 4.2 3.1 - - - +
398B ARG* 1.3 84.4 - - + +
400B ASN* 1.3 71.3 + - - +
401B LEU* 3.4 32.2 + - + +
525B PRO* 4.1 21.2 - - + +
572B LYS* 4.0 24.9 - - + +
573B ILE* 3.9 25.6 - - + -
612B GLU 5.0 2.0 - - - +
614B GLN* 4.9 13.0 - - + +
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Residues in contact with ASN 400 (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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396B ARG 3.0 13.8 + - - -
397B GLU* 3.3 25.1 + - - +
398B ARG 4.2 4.7 - - - +
399B LEU* 1.3 79.9 - - - +
401B LEU* 1.3 63.2 + - - +
402B PRO* 4.2 2.3 - - - +
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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