Contacts of the strand formed by residues 437 - 443 (chain B) in PDB entry 3EWS
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 GLY 437 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B THR 3.3 8.9 + - - +
307B ILE* 3.3 16.6 - - - +
308B LYS* 3.1 21.7 + - - +
403B SER 3.5 8.5 - - - -
429B ARG* 3.7 16.5 - - - +
435B LYS 3.7 2.6 + - - -
436B ARG* 1.3 81.6 - - - +
438B LEU* 1.3 63.0 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ILE* 3.8 4.2 - - - +
308B LYS* 3.3 32.8 - - + +
310B TYR* 3.5 29.2 - - + -
327B LEU* 5.2 1.6 - - + -
331B ILE* 4.1 28.3 - - + -
403B SER 3.1 10.4 + - - +
404B VAL* 3.5 17.0 - - + -
405B VAL* 2.9 27.0 + - - +
427B ILE* 5.0 1.4 - - - +
429B ARG* 5.0 1.4 - - - +
437B GLY* 1.3 75.8 - - - +
439B ALA* 1.3 64.1 + - - +
440B VAL* 4.4 13.9 - - + -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ILE* 4.0 1.5 - - + +
308B LYS 2.8 11.9 + - - +
309B GLN* 4.7 4.9 - - + -
310B TYR* 3.0 26.7 + - - +
405B VAL* 3.4 6.7 - - + +
407B ASN* 5.5 0.7 - - - +
423B TYR* 4.5 12.1 - - - +
427B ILE* 3.6 39.7 - - + -
438B LEU* 1.3 73.2 - - - +
440B VAL* 1.3 68.6 + - - +
441B ASN* 4.5 3.6 - - - +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B TYR* 3.8 13.2 - - + -
312B VAL* 4.3 24.5 - - + -
327B LEU* 4.2 21.8 - - + -
405B VAL 2.9 7.9 + - - -
406B ILE* 3.4 27.9 - - + +
407B ASN 3.0 22.8 + - - +
438B LEU* 4.4 17.5 - - + -
439B ALA* 1.3 82.4 - - - +
441B ASN* 1.3 65.5 + - - +
442B MET* 4.3 18.2 - - + -
466B LEU* 5.9 3.6 - - + -
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Residues in contact with ASN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B TYR 3.0 20.8 + - - +
311B TYR* 3.1 4.8 - - + +
312B VAL 3.0 25.3 + - - -
407B ASN* 3.0 30.0 + - - +
410B LEU* 3.0 22.6 - - + +
423B TYR* 3.3 24.8 + - - -
439B ALA* 4.5 3.4 - - - +
440B VAL* 1.3 81.4 - - - +
442B MET* 1.3 64.0 + - - +
452B LEU* 3.6 26.4 - - + +
463B ILE* 4.4 2.4 - - - +
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Residues in contact with MET 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B VAL* 3.8 17.5 - - + +
314B CYS* 4.9 1.3 - - - -
320B LYS* 3.2 41.7 + - + +
323B ALA* 4.2 11.4 - - + -
324B LEU* 4.1 29.8 - - + +
327B LEU* 5.0 2.5 - - + -
406B ILE* 3.9 22.2 - - + -
407B ASN 3.2 7.0 + - - +
408B PHE* 3.4 30.9 - - + +
409B ASP* 4.9 0.2 - - - -
410B LEU* 3.1 19.8 + - - +
440B VAL* 4.3 16.8 - - + -
441B ASN* 1.3 76.8 - - - +
443B VAL* 1.3 61.1 + - - +
444B ASP* 4.1 2.4 + - - -
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TYR* 3.7 30.3 - - + -
312B VAL 3.1 9.2 + - - +
313B LEU* 3.6 14.6 - - + +
314B CYS* 2.8 29.4 + - - +
410B LEU* 4.6 3.4 - - + -
441B ASN 4.1 5.6 - - - +
442B MET* 1.3 76.8 - - - +
444B ASP* 1.3 59.3 + - - +
445B SER 3.6 5.8 - - - +
448B SER* 3.2 19.5 - - - +
449B MET* 3.6 33.0 - - + +
452B LEU* 4.1 18.8 - - + -
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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