Contacts of the strand formed by residues 385 - 391 (chain B) in PDB entry 1QAS
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 VAL 385 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333B LEU* 4.7 3.4 - - + -
338B ARG* 3.0 24.2 - - - +
340B LEU* 4.5 9.6 - - + -
373B ILE* 4.8 2.9 - - + -
377B ALA* 3.6 31.2 - - + +
378B PHE* 3.7 21.3 - - + -
384B PRO* 1.3 74.4 - - - +
386B ILE* 1.3 61.3 + - - +
387B LEU* 3.8 25.4 - - + -
434B LYS 3.3 3.0 + - - -
435B ILE* 3.2 20.3 - - + +
436B LEU* 3.0 24.3 + - - +
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU* 4.9 8.1 - - + -
307B VAL* 5.2 2.7 - - + -
338B ARG 2.8 6.2 + - - +
339B CYS* 3.4 28.5 - - + -
340B LEU 2.9 27.0 + - - +
384B PRO* 5.0 1.1 - - + +
385B VAL* 1.3 76.7 - - - +
387B LEU* 1.3 65.1 + - - +
388B SER* 4.4 3.6 - - - +
436B LEU* 3.3 22.2 - - + +
438B LYS* 3.9 26.2 - - + -
499B CYS* 4.4 18.6 - - - -
520B MET* 6.0 0.9 - - - -
547B LEU* 4.7 8.3 - - + -
574B ILE* 4.2 16.2 - - + -
601B TYR* 4.5 14.4 - - + +
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Residues in contact with LEU 387 (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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340B LEU* 3.6 25.6 - - + -
342B LEU* 4.2 11.4 - - + -
370B LEU* 4.0 27.4 - - + -
373B ILE* 3.9 20.0 - - + -
385B VAL* 3.8 16.8 - - + -
386B ILE* 1.3 76.8 - - - +
388B SER* 1.3 62.8 + - - +
389B LEU* 3.4 8.3 + - + +
405B LEU* 4.7 0.9 - - + -
409B LEU* 4.4 4.7 - - + -
435B ILE* 3.7 22.7 - - + -
436B LEU 2.8 9.3 + - - -
437B LEU* 3.4 21.1 - - + -
438B LYS 2.9 23.3 + - - +
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Residues in contact with SER 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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339B CYS* 5.0 4.0 - - - +
340B LEU 2.7 20.2 + - - -
341B GLU* 3.1 22.7 - - - +
342B LEU* 2.9 30.1 + - - +
386B ILE* 3.8 5.3 + - - +
387B LEU* 1.3 69.4 - - - +
389B LEU* 1.3 61.5 + - - +
390B GLU 4.0 0.2 + - - -
438B LYS* 3.6 34.5 - - - +
520B MET* 5.8 0.2 - - - -
549B ARG* 4.8 9.8 + - - -
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Residues in contact with LEU 389 (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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342B LEU* 3.6 32.8 - - + +
344B CYS* 4.4 5.6 - - - -
366B PHE* 4.3 15.3 - - + -
387B LEU* 3.8 14.1 - - + +
388B SER* 1.3 74.3 - - - +
390B GLU* 1.3 60.0 + - - +
391B ASN* 3.7 6.8 + - + +
401B MET* 4.5 10.8 - - + -
405B LEU* 4.4 12.3 - - + -
437B LEU* 4.2 31.0 - - + -
438B LYS* 2.8 23.4 + - - +
439B GLY* 3.9 12.8 - - - -
440B LYS 5.1 0.3 + - - -
492B LEU* 4.6 10.5 - - + -
496B ILE* 4.8 6.3 - - + -
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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
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312B ASN* 5.8 0.3 + - - -
342B LEU 2.9 8.1 + - - -
343B ASP* 3.4 34.7 - - - +
344B CYS* 2.9 24.7 + - - -
345B TRP* 4.9 2.6 - - - -
356B HIS* 6.0 1.0 - - - -
388B SER 4.0 0.8 + - - +
389B LEU* 1.3 71.4 - - - +
391B ASN* 1.3 58.3 + - - +
392B HIS* 2.9 37.0 + - + +
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Residues in contact with ASN 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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344B CYS* 3.9 4.2 - - + +
389B LEU* 3.7 7.5 + - + +
390B GLU* 1.3 72.3 - - - +
392B HIS* 1.3 66.4 + - - +
393B CYS* 3.2 23.2 - - - +
398B GLN* 3.1 35.1 + - - +
401B MET* 3.2 34.3 - - + -
488B LEU* 4.6 5.9 - - + +
492B LEU* 3.9 11.8 - - + +
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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