Contacts of the strand formed by residues 320 - 325 (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 GLN 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LEU 3.6 4.5 - - - +
288A MET* 3.4 38.1 - - + +
292A PHE* 5.7 1.3 - - - -
318A GLN 3.7 12.2 + - - +
319A ALA* 1.3 74.5 - - - +
321A VAL* 1.4 62.2 + - - +
322A THR* 5.6 5.6 - - + -
347A LYS 4.3 0.4 - - - -
348A PHE* 3.6 3.1 - - - +
349A LEU* 2.8 70.9 + - + +
350A PHE* 5.0 2.4 - - - -
351A PRO* 4.8 3.0 - - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU 4.1 0.3 - - - +
286A SER* 3.4 2.8 - - - -
287A LEU* 2.9 52.2 + - + +
292A PHE* 3.4 33.0 - - + -
320A GLN* 1.4 75.5 - - - +
322A THR* 1.4 65.2 + - - +
323A VAL* 4.4 0.8 - - - +
346A VAL* 4.0 8.7 - - + -
347A LYS 3.2 11.2 - - - +
348A PHE* 3.6 28.5 - - + -
502A 2OB 3.7 27.8 - - + -
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU 3.5 6.3 - - - -
286A SER* 3.3 23.1 - - - +
288A MET* 6.6 0.4 - - + -
320A GLN* 5.6 5.8 - - + +
321A VAL* 1.4 76.0 - - - +
323A VAL* 1.3 62.8 + - - +
324A HIS* 4.2 5.8 + - - -
345A MET 3.2 4.9 - - - +
346A VAL* 3.4 1.0 - - - -
347A LYS* 2.9 61.1 + - + +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A MET* 3.2 5.4 - - - +
285A LEU* 2.8 44.3 + - + +
321A VAL* 4.8 1.6 - - + -
322A THR* 1.3 79.6 - - - +
324A HIS* 1.3 63.7 + - - +
344A VAL* 4.3 8.5 - - + -
345A MET 3.3 3.1 - - - +
346A VAL* 4.0 14.4 - - + -
421A VAL* 5.9 0.2 - - + -
502A 2OB 3.6 63.3 - - + -
503A DLP 3.8 21.4 - - + +
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Residues in contact with HIS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU 3.6 6.1 - - - +
284A MET* 3.8 23.6 - - + -
322A THR* 5.1 7.9 + - - -
323A VAL* 1.3 76.4 - - - +
325A CYS* 1.3 78.4 + - - +
326A LEU* 4.0 12.1 - - + +
344A VAL* 3.6 5.7 - - - +
345A MET* 3.0 59.1 + - + +
347A LYS* 4.9 11.4 - - + +
503A DLP 5.3 0.4 - - - -
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Residues in contact with CYS 325 (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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278A PHE* 3.3 24.1 - - + -
283A LEU* 3.2 20.1 + - + +
284A MET* 6.0 0.2 - - - +
324A HIS* 1.3 85.7 - - - +
326A LEU* 1.3 63.0 + - - +
327A LYS 3.6 18.4 - - - +
329A PRO* 4.1 17.0 - - - -
342A SER* 4.4 4.9 - - - -
343A SER 3.7 3.4 - - - -
344A VAL* 4.2 6.5 - - - -
503A DLP 3.3 37.0 - - - -
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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