Contacts of the strand formed by residues 405 - 414 (chain A) in PDB entry 1QU2
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 ILE 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A TYR* 3.5 1.3 - - - -
185A TRP* 2.6 52.9 + - + +
187A PRO* 4.1 18.6 - - + -
235A TRP* 3.4 34.1 - - + -
349A ILE* 4.4 22.7 - - + -
367A TYR* 3.5 39.9 - - + -
394A TYR* 4.1 8.7 - - + +
404A VAL* 1.3 82.2 - - - +
406A PHE* 1.3 68.3 + - - +
407A ARG* 5.0 5.2 - - + -
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 4.2 19.5 - - + -
183A VAL* 3.5 13.5 - - - -
184A TYR* 3.7 36.8 - + - -
235A TRP* 4.0 8.3 - - - -
330A HIS* 2.9 51.5 + - + +
331A GLY* 4.2 1.1 - - - +
332A GLU* 4.2 37.5 - - + -
394A TYR* 5.3 3.1 + - - -
395A PRO* 5.7 5.2 - - + -
404A VAL* 6.1 0.2 - - + -
405A ILE* 1.3 77.3 - - - +
407A ARG* 1.3 62.5 + - - +
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Residues in contact with ARG 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.8 3.8 - - - -
183A VAL* 2.9 31.0 + - - +
185A TRP* 3.1 66.7 - - + +
329A GLY 3.8 6.0 + - - -
330A HIS* 4.2 4.5 - - + -
348A PRO 4.2 10.7 + - - +
349A ILE* 2.6 36.5 + - + -
350A ASP* 2.9 26.6 - - - +
351A ASP* 3.2 12.5 + - - +
405A ILE* 5.0 4.9 - - + -
406A PHE* 1.3 78.6 - - - +
408A ALA* 1.3 74.7 + - - +
409A THR* 3.4 3.7 + - - -
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 4.6 14.5 - - + +
181A LYS 3.2 15.0 - - - +
182A PRO* 3.8 2.2 - - + -
328A PRO 4.6 8.1 - - - +
329A GLY* 3.5 14.9 + - - +
335A TYR* 6.3 1.3 - - + -
345A VAL* 4.1 25.4 - - + -
346A ILE 5.7 0.4 - - - +
407A ARG* 1.3 83.3 + - - +
409A THR* 1.3 60.0 + - - +
410A PRO* 4.8 1.0 - - - +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LYS* 3.1 4.2 - - - -
181A LYS 2.6 35.4 + - - -
183A VAL* 4.0 15.7 - - + +
185A TRP* 3.8 24.9 - - + -
407A ARG* 4.4 4.2 + - - -
408A ALA* 1.3 75.4 + - - +
410A PRO* 1.3 84.8 - - + +
411A GLN* 3.0 29.5 + - - +
456A GLN* 4.4 9.9 - - + +
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Residues in contact with PRO 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LYS* 3.9 24.7 - - - +
179A GLY 3.2 14.8 - - - +
180A LYS* 3.9 14.6 - - + -
408A ALA 4.8 0.9 - - - +
409A THR* 1.3 104.3 - - + +
411A GLN* 1.3 62.8 + - - +
412A TRP* 5.8 0.9 - - - -
456A GLN* 4.2 5.2 + - - -
523A ASP* 4.5 3.5 - - - +
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Residues in contact with GLN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LYS* 3.6 3.2 - - - +
179A GLY 2.8 30.5 + - - -
181A LYS* 4.1 17.3 - - + +
183A VAL* 4.2 11.6 - - + +
409A THR* 3.0 28.9 + - + +
410A PRO* 1.3 81.0 - - - +
412A TRP* 1.3 64.9 + - - +
413A PHE* 3.5 19.0 - - + -
452A VAL* 4.2 13.9 - - + +
454A SER* 2.6 41.5 + - - +
456A GLN* 2.9 34.6 + - - +
523A ASP* 5.1 0.2 - - - -
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Residues in contact with TRP 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 3.8 13.9 - - + -
177A TYR* 3.6 20.4 - - - -
178A LYS* 3.8 28.6 - - + +
410A PRO 5.7 0.2 - - - -
411A GLN* 1.3 78.3 - - - +
413A PHE* 1.3 62.8 + - - +
452A VAL* 3.6 6.2 - - - +
453A ILE* 3.0 33.0 + - + -
454A SER* 2.9 11.7 + - - +
463A LEU* 3.4 34.2 - - + +
465A VAL* 3.9 26.2 - - + -
467A TYR* 3.3 21.4 + + - -
473A ILE* 3.9 28.3 - - + -
475A MET* 4.0 22.0 - - + -
521A GLU* 3.2 20.2 + - - -
523A ASP* 3.9 17.5 - - - -
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU 3.7 0.3 - - - +
176A ILE* 3.4 9.5 - - - +
177A TYR* 2.9 74.8 + + + +
179A GLY* 4.0 3.8 - - - -
180A LYS 3.6 33.7 - - - -
181A LYS* 4.1 15.0 - - + -
335A TYR* 4.8 7.9 - + - -
411A GLN* 3.5 25.4 - - + -
412A TRP* 1.3 77.2 - - - +
414A ALA* 1.3 62.6 + - - +
450A GLU* 4.1 15.7 - - + -
451A TRP 3.2 7.2 - - - +
452A VAL* 3.8 28.7 - - + -
453A ILE* 4.3 4.8 - - - +
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A MET* 4.2 19.1 - - + -
175A LEU 3.3 5.4 - - - -
176A ILE* 4.8 2.0 - - + +
413A PHE* 1.3 73.6 - - - +
415A SER* 1.3 59.3 + - - +
416A ILE* 3.0 9.7 + - + +
450A GLU* 3.0 11.0 - - - +
451A TRP* 2.8 48.6 + - + -
453A ILE* 3.9 17.0 - - + -
529A PHE* 5.6 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