Contacts of the strand formed by residues 407 - 416 (chain B) in PDB entry 1QXP
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 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B LEU* 3.7 38.8 - - + +
392B GLU 3.9 1.1 - - - -
393B GLU 2.8 29.6 - - - +
394B VAL* 4.2 1.8 - - - +
395B ASP* 4.1 2.9 - - - -
406B GLY* 1.3 75.9 - - - -
408B SER* 1.4 59.0 + - - +
409B PHE 4.3 0.4 - - - -
476B ILE 4.1 0.2 - - - +
477B ARG* 3.4 4.5 - - - -
478B LEU 2.8 40.2 + - - +
480B PRO* 3.7 25.6 - - - -
506B LYS* 6.4 0.7 - - + -
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Residues in contact with SER 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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230B LYS* 4.9 5.2 + - - -
356B TRP* 5.0 1.1 - - - -
391B LEU* 5.3 1.4 - - - +
395B ASP* 3.1 30.2 + - - -
407B CYS* 1.4 67.6 - - - +
409B PHE* 1.4 62.4 + - - +
475B ARG* 5.2 11.5 - - - +
476B ILE 3.6 5.2 + - - -
477B ARG* 3.5 22.9 + - - +
504B SER* 3.8 1.9 - - - -
505B GLU* 2.9 40.6 + - - +
506B LYS 4.9 0.3 + - - -
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Residues in contact with PHE 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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356B TRP* 5.5 1.8 - - - -
389B ILE* 4.0 17.7 - - + -
391B LEU* 4.1 24.2 - - + -
408B SER* 1.4 60.9 - - - +
410B LEU* 1.4 67.6 + - - +
411B LEU* 4.1 14.4 - - + -
435B VAL* 5.0 3.8 - - + -
475B ARG* 3.4 3.8 - - - +
476B ILE* 2.6 78.3 + - + +
478B LEU* 4.0 16.2 - - + -
502B PHE* 3.8 38.8 - + - -
503B PHE 3.6 5.4 - - - +
504B SER* 3.4 21.1 - - - +
505B GLU 4.9 0.2 - - - +
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Residues in contact with LEU 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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211B VAL* 3.7 31.6 - - + -
212B THR 5.8 0.4 - - - +
213B GLU* 3.6 28.3 - - + +
341B CYS* 3.9 9.9 - - + -
356B TRP* 4.1 8.9 - - + -
409B PHE* 1.4 72.8 - - - +
411B LEU* 1.3 63.1 + - - +
412B ALA* 5.2 0.2 - - - +
473B SER* 6.6 0.2 - - - -
474B ASN 3.6 7.2 - - - +
475B ARG* 3.1 52.0 - - + +
501B ARG 3.5 4.2 - - - +
502B PHE* 3.6 2.3 - - - -
503B PHE* 3.0 54.1 + - + +
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Residues in contact with LEU 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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409B PHE* 4.0 19.3 + - + -
410B LEU* 1.3 74.9 - - - +
412B ALA* 1.4 62.8 + - - +
433B PHE* 3.8 31.1 - - + -
435B VAL* 3.6 31.0 - - + -
473B SER* 3.0 4.5 - - - -
474B ASN 2.8 35.3 + - - +
475B ARG* 4.8 0.2 - - - +
476B ILE* 4.3 6.7 - - + -
485B VAL* 4.4 10.8 - - + -
500B LEU* 4.3 13.9 - - + -
501B ARG 3.6 7.9 - - - +
502B PHE* 3.0 40.2 - - + -
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Residues in contact with ALA 412 (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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211B VAL* 3.7 26.5 - - + -
410B LEU 5.2 0.4 - - - +
411B LEU* 1.4 76.1 - - - +
413B LEU* 1.3 62.9 + - - +
433B PHE* 5.1 0.2 - - - -
471B GLU* 4.3 10.1 - - - +
472B VAL 3.5 0.4 - - - -
473B SER* 3.1 24.2 - - - -
499B LEU 3.3 2.6 - - - +
500B LEU* 3.1 9.1 - - - +
501B ARG* 2.9 45.3 + - + +
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Residues in contact with LEU 413 (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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365B TRP* 3.7 19.5 - - + -
412B ALA* 1.3 77.4 - - - +
414B MET* 1.3 66.0 + - - +
431B ILE* 4.1 16.0 - - + +
432B GLY 3.7 20.0 - - - +
433B PHE* 4.6 7.4 - - + -
471B GLU* 3.0 3.6 - - - -
472B VAL* 2.5 46.6 + - + +
487B PRO* 3.5 21.3 - - + -
488B SER 3.9 0.4 - - - +
498B PHE* 3.3 42.2 - - + -
499B LEU 3.8 1.8 - - - +
500B LEU* 3.7 22.2 - - + -
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Residues in contact with MET 414 (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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144B TRP* 3.5 24.2 - - + -
146B PHE* 3.3 54.1 - - + +
205B GLU* 4.3 4.5 - - - +
413B LEU* 1.3 81.8 - - - +
415B GLN* 1.3 69.3 + - - +
416B LYS* 5.3 0.6 - - + +
431B ILE* 4.7 2.0 - - - -
470B ARG* 3.5 28.5 - - - +
471B GLU* 3.8 31.2 - - + +
498B PHE* 3.1 28.4 - - - +
499B LEU* 3.4 25.0 + - + +
501B ARG* 5.8 0.4 - - - -
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Residues in contact with GLN 415 (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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146B PHE* 3.8 15.1 - - - -
365B TRP* 5.3 3.8 - - + -
414B MET* 1.3 79.4 - - - +
416B LYS* 1.4 60.7 + - - +
417B HIS* 4.3 0.6 - - - -
428B MET* 3.2 26.1 - - + +
429B GLU* 2.8 51.1 + - - +
431B ILE* 3.6 18.7 - - + +
469B LEU 2.7 25.8 + - - +
470B ARG* 2.7 22.6 + - - +
496B GLY* 6.5 0.4 - - - -
497B ASP 3.5 10.1 - - - +
498B PHE* 5.2 1.6 - - + -
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Residues in contact with LYS 416 (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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145B GLN 5.5 0.4 + - - -
146B PHE* 3.4 48.0 + - + +
148B GLU* 4.4 13.3 + - - +
362B GLU* 3.0 31.9 + - - +
414B MET* 5.4 1.1 - - + -
415B GLN* 1.4 72.3 - - - +
417B HIS* 1.3 67.1 + - - +
418B ARG* 4.0 23.1 + - - +
497B ASP* 3.2 50.3 + - + +
498B PHE* 4.7 9.9 - - - +
499B LEU* 5.1 4.5 - - + -
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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