Contacts of the strand formed by residues 330 - 334 (chain A) in PDB entry 2EWY
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 GLU 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A CYS* 3.4 1.9 - - - +
283A TRP* 2.9 30.1 + - - +
285A ASN 4.5 5.2 - - - +
286A SER 5.4 2.4 - - - +
287A GLU 5.7 0.3 - - - +
288A THR* 5.2 6.7 - - - +
321A PRO* 4.4 7.8 - - + +
322A MET 3.1 18.8 - - - +
324A GLY* 3.6 8.5 - - - +
328A ASN* 3.3 1.4 - - - +
329A TYR* 1.3 103.3 - - - +
331A CYS* 1.3 66.5 + - - +
332A TYR* 3.4 37.0 + - + +
63B TYR* 5.6 0.2 + - - -
127B PRO* 4.2 12.6 - - - +
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Residues in contact with CYS 331 (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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280A LEU* 4.3 5.4 - - + -
281A ALA 3.0 7.6 - - - +
282A CYS* 2.0 46.0 - - - -
321A PRO* 3.3 2.8 - - - +
322A MET* 2.6 47.4 + - + +
323A MET 4.5 2.2 - - - -
324A GLY 4.0 17.0 - - - -
328A ASN* 4.6 2.5 - - - -
330A GLU* 1.3 77.8 - - - +
332A TYR* 1.3 60.6 + - - +
280B LEU* 3.9 21.3 - - + -
322B MET* 4.6 2.2 - - + -
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Residues in contact with TYR 332 (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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270A PHE* 5.2 4.9 - + + -
274A PHE* 3.3 10.5 - - + -
280A LEU* 3.4 7.2 - - - -
281A ALA* 2.6 42.7 + - + +
283A TRP* 3.8 25.5 - + + +
287A GLU 5.0 0.2 + - - -
288A THR* 4.0 9.9 - - - +
289A PRO* 3.1 40.1 - - + +
290A TRP* 4.4 12.6 - + - -
319A ILE* 3.7 34.5 - - + -
320A GLN 3.1 6.3 - - - +
321A PRO* 3.6 30.3 - - + -
322A MET* 5.0 0.4 - - - -
330A GLU* 3.4 31.1 + - + +
331A CYS* 1.3 74.8 - - - +
333A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 333 (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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26A SER* 3.3 27.5 + - - -
27A GLY* 4.1 10.7 - - - +
245A THR* 5.4 3.2 - - - +
246A LEU* 4.9 7.2 - - - +
274A PHE* 3.8 5.3 - - - -
277A GLY* 6.5 1.1 - - - -
279A GLN 5.0 0.9 - - - +
280A LEU* 3.4 24.0 - - + +
319A ILE* 3.7 4.7 - - - -
320A GLN* 2.8 67.0 + - - +
321A PRO 4.0 10.7 + - - -
322A MET* 3.1 38.7 - - + +
332A TYR* 1.3 73.5 - - - +
334A PHE* 1.3 64.4 + - - +
335A GLY 3.5 0.7 + - - -
325B ALA* 4.2 20.0 - - - +
326B GLY* 5.3 4.3 - - - +
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Residues in contact with PHE 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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246A LEU* 4.1 12.0 - - - +
254A PHE* 3.8 15.5 - + - -
257A VAL* 5.3 0.9 - - + -
258A VAL* 4.2 8.3 - - + -
261A VAL* 5.0 8.3 - - + -
274A PHE* 3.5 34.5 + + + +
275A TRP* 3.5 52.3 - + - +
277A GLY* 5.5 6.4 - - - +
279A GLN 5.4 0.6 + - - -
318A TYR* 3.8 22.0 - + - -
319A ILE* 4.3 2.7 - - + -
320A GLN* 4.5 0.6 - - - +
333A ARG* 1.3 76.4 - - - +
335A GLY* 1.3 60.6 + - - +
336A ILE* 3.0 67.6 + - + +
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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