Contacts of the strand formed by residues 2 - 7 (chain A) in PDB entry 4QY2
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 LYS 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP* 1.3 75.7 - - - +
3A ILE* 1.3 61.0 + - - +
4A CYS* 4.2 15.9 - - - -
348B ARG 4.2 0.2 - - - +
349B HIS* 3.3 1.9 - - - -
350B GLN* 2.8 60.1 + - + +
456B ASP* 4.2 13.5 + - - +
460B CYS* 4.1 17.1 - - + -
461B PHE 3.2 15.3 - - - +
462B GLU* 4.0 20.4 + - + +
463B ILE* 4.3 2.9 - - - +
472B MET* 3.7 6.1 - - - +
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Residues in contact with ILE 3 (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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2A LYS* 1.3 76.5 - - - +
4A CYS* 1.3 66.9 + - - +
5A LEU* 5.2 0.9 - - + -
347B PHE* 3.8 33.9 - - + -
348B ARG 3.5 7.6 - - - +
349B HIS* 4.1 8.7 - - + -
445B VAL* 4.9 4.0 - - + -
449B LEU* 4.6 7.0 - - + -
460B CYS* 3.4 0.5 - - - -
461B PHE* 2.8 54.3 + - + -
463B ILE* 4.0 15.9 - - + +
472B MET* 4.2 22.0 - - + +
475B ILE* 4.0 24.0 - - + -
476B ARG* 4.5 7.0 - - + +
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Residues in contact with CYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 4.2 18.2 - - - -
3A ILE* 1.3 77.5 - - - +
5A LEU* 1.3 66.0 + - - +
337B TRP* 3.6 14.8 - - + -
347B PHE* 3.3 8.0 - - - +
348B ARG* 2.6 44.7 + - + +
459B GLY 3.6 3.6 - - - +
460B CYS* 2.0 42.6 - - - -
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Residues in contact with LEU 5 (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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3A ILE* 4.6 2.9 - - + +
4A CYS* 1.3 81.0 - - - +
6A GLY* 1.3 56.6 + - - +
333B LEU* 3.8 19.5 - - + +
337B TRP* 3.7 7.5 - - - -
346B GLY 3.6 4.5 - - - +
347B PHE* 3.5 33.4 - - + -
438B MET* 4.1 10.1 - - + -
441B LEU* 3.7 27.6 - - + -
442B TYR* 4.1 23.6 - - + -
445B VAL* 4.2 11.7 - - + -
458B LYS 5.0 0.9 - - - +
459B GLY* 2.9 15.2 + - - +
461B PHE* 3.5 35.4 - - + -
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Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 1.3 76.6 - - - +
7A HIS* 1.3 61.1 + - - -
333B LEU* 4.3 5.8 - - - -
335B ASN 5.8 1.6 - - - -
337B TRP* 3.5 21.3 - - - -
345B TYR* 3.3 4.5 - - - -
346B GLY 2.9 32.6 + - - -
438B MET* 3.4 16.6 - - - +
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Residues in contact with HIS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY* 1.3 75.6 - - - +
8A HIS* 1.3 70.0 + - - +
313A MET* 3.4 20.5 - - - -
314A ARG 4.6 2.0 - - - -
316A VAL* 3.9 16.2 - - + +
329B ILE* 3.7 40.5 - - + +
330B ALA 4.5 1.6 + - - -
333B LEU* 3.9 20.3 - - + +
335B ASN* 3.8 16.0 + - - -
336B GLY* 3.2 26.3 - - - -
337B TRP* 2.7 33.1 + - - +
340B MET* 3.7 6.5 - - - +
344B TRP 3.1 13.2 - - - +
345B TYR* 4.1 4.0 - - + -
438B MET* 4.0 8.7 - - - -
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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