Contacts of the strand formed by residues 404 - 411 (chain B) in PDB entry 2CXQ
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 CYS 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B HIS* 5.0 0.2 - - - -
337B ALA* 3.4 21.8 - - - -
339B LEU* 3.9 15.7 - - + -
395B ILE* 4.1 20.4 - - - -
402B ILE* 3.3 21.9 + - - -
403B PRO* 1.3 74.3 - - - +
405B ASP* 1.3 65.0 + - - +
406B PHE* 3.7 24.2 - - + -
436B LEU* 5.2 0.7 - - - -
473B PRO 3.7 5.3 + - - -
474B THR* 3.3 10.6 - - + -
475B ASN* 2.9 26.3 + - - +
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Residues in contact with ASP 405 (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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320B LEU* 5.0 3.3 - - - +
336B HIS* 3.0 30.3 + - - -
337B ALA 2.9 8.9 + - - -
338B LEU* 3.9 9.2 - - + -
339B LEU* 2.8 29.1 + - - +
404B CYS* 1.3 72.7 - - - +
406B PHE* 1.3 62.1 + - - +
407B LEU* 3.6 6.7 - - + +
475B ASN* 2.9 34.0 - - - +
477B ILE* 4.4 8.4 - - + +
494B TYR* 2.7 36.2 + - - +
497B LYS* 4.5 1.4 + - - -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.5 13.7 - - + -
341B TYR* 3.5 39.9 - + - -
392B TYR* 3.5 19.3 - + - -
395B ILE* 6.3 0.2 - - + -
404B CYS* 3.7 24.5 - - + -
405B ASP* 1.3 76.7 - - - +
407B LEU* 1.3 55.6 + - - +
429B PHE* 3.4 23.7 - + + -
432B GLN* 3.8 14.1 - - + -
433B THR* 3.6 22.7 - - + -
436B LEU* 3.8 19.5 - - + -
474B THR* 3.8 16.4 - - + -
475B ASN 2.9 13.0 + - - +
476B SER* 3.4 0.7 - - - +
477B ILE* 2.7 32.7 + - - +
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Residues in contact with LEU 407 (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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338B LEU* 4.8 3.4 - - + -
339B LEU 3.2 9.7 + - - +
340B PRO* 4.1 26.9 - - + +
341B TYR* 2.6 34.3 + - - +
342B ASP* 5.4 0.2 - - - +
345B MET* 4.6 6.3 - - + -
348B PHE* 4.3 20.2 - - + -
405B ASP* 3.6 19.5 - - + +
406B PHE* 1.3 76.7 - - - +
408B ILE* 1.3 60.7 + - - +
429B PHE* 3.5 1.5 - - - -
477B ILE* 3.2 28.7 - - + +
479B PHE* 4.1 13.7 - - + -
490B LEU* 4.9 4.9 - - + -
494B TYR* 4.0 32.3 - - + +
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Residues in contact with ILE 408 (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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549A ILE* 6.0 0.4 - - + -
341B TYR* 3.5 32.5 - - + +
407B LEU* 1.3 75.3 - - - +
409B PRO* 1.3 75.7 - - + +
422B HIS* 4.6 1.8 - - + -
425B LEU* 3.9 18.8 - - + -
426B LEU* 3.8 28.9 - - + -
429B PHE* 3.6 42.8 - - + -
477B ILE 3.1 7.3 + - - -
478B VAL* 3.4 15.6 - - + +
479B PHE* 3.1 29.7 + - - -
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Residues in contact with PRO 409 (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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341B TYR 4.1 5.4 - - - +
342B ASP* 3.5 30.1 - - + +
408B ILE* 1.3 97.7 - - + +
410B VAL* 1.3 59.1 + - - +
411B GLN 3.5 19.1 - - - +
412B THR* 5.4 1.6 - - - -
422B HIS* 2.9 30.4 + - + -
426B LEU* 4.2 1.2 - - - +
479B PHE* 3.2 28.5 - - + +
481B LYS* 4.0 0.7 - - - -
482B LEU* 3.8 17.5 - - + +
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Residues in contact with VAL 410 (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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548A PHE* 3.9 18.2 - - + -
549A ILE* 3.5 39.0 - - + +
552A GLN* 4.0 7.9 - - + +
553A ARG* 3.7 26.8 - - + +
1702A GOL 5.2 1.4 + - - -
408B ILE 3.9 0.2 + - - -
409B PRO* 1.3 71.9 - - - +
411B GLN* 1.3 57.1 + - - +
422B HIS* 3.0 21.5 + - - -
426B LEU* 4.1 10.0 - - - +
478B VAL* 3.6 22.2 - - + -
479B PHE 2.7 18.1 + - - +
480B THR* 3.5 9.4 - - - +
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Residues in contact with GLN 411 (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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552A GLN 2.9 23.2 + - - -
553A ARG* 3.5 26.7 + - + +
555A THR 2.7 29.6 + - - +
557A LEU* 5.1 2.5 + - - +
409B PRO* 3.5 18.7 - - - +
410B VAL* 1.3 79.0 - - - +
412B THR* 1.3 64.2 + - - +
413B GLN* 4.1 0.9 + - - +
422B HIS* 4.1 1.6 - - - -
480B THR* 2.8 25.5 + - - +
481B LYS* 3.8 38.0 + - + +
482B LEU 4.6 0.2 + - - -
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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