Contacts of the strand formed by residues 330 - 334 (chain A) in PDB entry 4EWS
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 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A HIS* 5.1 8.3 - - + +
327A LYS* 3.6 37.2 - - - +
328A MET* 4.1 16.4 - - + +
329A PRO* 1.3 71.4 - - - +
331A ILE* 1.3 61.0 + - - +
332A SER* 4.5 3.1 + - - -
339A VAL 3.5 5.0 - - - +
341A ASP* 2.9 68.6 + - + +
343A SER* 6.2 2.0 - - - +
366A ASP* 5.4 5.1 + - - -
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.7 11.5 - - - +
270A PHE* 3.4 48.7 - - + +
271A HIS* 4.6 18.1 - - - +
273A LEU* 5.3 0.9 - - + -
274A ALA* 3.7 19.1 - - + -
329A PRO* 3.6 3.4 + - + +
330A LYS* 1.3 74.8 - - - +
332A SER* 1.3 67.1 + - - +
338A VAL* 3.5 29.2 - - + -
339A VAL 3.4 3.6 - - - +
340A VAL* 4.2 17.3 - - + -
502A 2OB 5.0 6.1 - - + -
503A DLP 3.9 26.2 - - + -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.6 15.0 - - - -
330A LYS 4.5 3.3 + - - -
331A ILE* 1.3 77.0 - - - +
333A CYS* 1.3 64.1 + - - +
334A GLN* 3.8 9.1 + - - -
338A VAL* 3.6 2.9 - - - -
339A VAL* 2.9 59.3 + - - +
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Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLU* 3.0 30.3 + - + +
270A PHE* 3.8 25.6 - - - -
332A SER* 1.3 72.6 - - - +
334A GLN* 1.3 66.8 + - - +
337A GLY 4.2 2.5 - - - -
338A VAL* 4.8 12.3 - - - +
450A THR* 5.1 1.6 - - + -
451A ARG 3.2 15.3 - - - +
452A ASP* 3.5 3.5 - - - +
453A GLY 3.1 17.3 + - - -
454A PHE 3.4 31.0 - - - +
455A LEU* 4.1 5.6 - - - -
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Residues in contact with GLN 334 (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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267A GLU* 5.6 0.4 + - - -
332A SER* 3.8 11.6 + - - -
333A CYS* 1.3 75.1 + - - +
335A ASN* 1.3 67.5 + - - +
336A LYS* 3.2 27.1 - - + -
337A GLY 2.9 26.1 + - - +
339A VAL* 3.3 24.4 - - + +
450A THR* 3.2 15.1 - - - -
451A ARG 3.7 6.7 - - - -
452A ASP* 3.1 31.4 + - + +
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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