Contacts of the strand formed by residues 541 - 547 (chain A) in PDB entry 6QNW
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ILE* 3.5 27.4 - - - -
324A LYS 3.4 15.0 - - - -
325A PRO* 3.9 9.6 - - - -
326A HIS* 4.1 9.4 - - + +
331A ASN* 4.3 3.6 - - - -
334A TYR* 3.7 40.2 - - + -
539A LYS 4.3 0.2 + - - -
540A TYR* 1.3 73.3 - - - +
542A VAL* 1.3 60.5 + - - +
543A LEU* 4.9 1.7 - - - +
563A LEU 3.7 1.7 - - - +
564A TYR* 3.8 0.5 - - - -
565A VAL* 2.9 41.4 + - - +
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Residues in contact with VAL 542 (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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322A ILE* 3.2 11.3 - - - +
323A VAL* 3.0 25.8 + - + -
324A LYS* 2.8 28.4 + - + +
530A PRO* 3.5 33.9 - - + -
537A TRP* 5.1 0.9 - - + -
540A TYR* 4.9 4.3 - - + +
541A CYS* 1.3 77.2 - - - +
543A LEU* 1.3 65.9 + - - +
562A PHE* 3.6 19.1 - - + -
563A LEU 3.6 2.9 - - - -
564A TYR* 3.4 42.4 - - + -
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Residues in contact with LEU 543 (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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320A PRO* 5.2 8.5 - - + -
322A ILE* 3.5 40.2 - - + +
334A TYR* 4.2 7.0 - - + +
335A LEU* 3.7 42.0 - - + +
338A TRP* 3.9 24.5 - - + -
541A CYS* 4.9 1.8 - - - +
542A VAL* 1.3 76.2 - - - +
544A GLU* 1.3 62.3 + - - +
545A ILE* 3.0 9.3 + - + +
563A LEU* 2.8 58.0 + - + +
565A VAL* 4.2 10.1 - - + -
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Residues in contact with GLU 544 (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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318A LYS* 2.6 29.1 + - - +
319A GLU 4.3 2.4 - - - +
320A PRO* 4.0 2.4 - - - +
321A TYR* 2.6 67.0 + - + +
323A VAL* 3.6 17.7 - - + +
531A ARG* 3.8 6.8 + - - -
542A VAL* 4.6 0.2 - - - +
543A LEU* 1.3 69.1 - - - +
545A ILE* 1.3 59.4 + - - +
546A GLY 4.6 1.8 - - - +
547A ASP* 4.2 0.3 - - - +
560A PRO* 3.7 15.7 - - + +
561A MET 4.4 1.6 - - - +
562A PHE* 3.3 42.9 - - + -
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Residues in contact with ILE 545 (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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317A TRP* 3.7 14.8 - - + -
318A LYS* 3.0 29.0 + - - +
320A PRO* 3.5 28.7 - - + -
338A TRP* 3.0 45.3 - - + +
342A LEU* 5.3 2.2 - - + -
525A PHE* 5.3 3.1 - - + -
543A LEU* 3.0 8.6 + - + +
544A GLU* 1.3 74.1 - - - +
546A GLY* 1.3 57.9 + - - +
561A MET* 2.9 41.4 + - + +
562A PHE 4.2 11.2 - - - -
563A LEU* 4.2 10.1 - - + -
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Residues in contact with GLY 546 (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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316A GLY 3.4 13.5 - - - -
318A LYS* 3.7 11.2 - - - +
544A GLU* 3.7 4.1 - - - +
545A ILE* 1.3 82.5 - - - +
547A ASP* 1.3 66.3 + - - +
560A PRO* 3.3 2.3 - - - +
561A MET* 2.5 43.2 + - - +
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Residues in contact with ASP 547 (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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314A PHE* 3.4 14.6 - - - -
315A PHE 3.9 5.5 - - - +
316A GLY* 3.4 11.5 + - - +
318A LYS* 3.5 26.8 + - - +
546A GLY* 1.3 85.3 - - - +
548A MET* 1.3 60.9 + - - +
558A SER* 3.9 21.1 + - - +
559A ARG 3.7 7.0 - - - +
560A PRO* 3.5 16.1 - - - +
561A MET 4.2 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