Contacts of the strand formed by residues 348 - 353 (chain B) in PDB entry 3EI1
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 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B HIS* 4.9 0.3 - - - +
324B GLU* 3.6 24.1 + - - +
342B THR* 4.8 0.3 - - - +
343B THR* 3.8 0.2 - - - -
344B ASP* 2.7 52.9 + - - +
347B ASN* 1.3 82.9 - - - +
349B ILE* 1.3 59.6 + - - +
350B ARG* 2.6 46.5 + - - -
363B ILE* 3.8 25.3 - - + +
364B ILE 3.4 1.8 - - - -
365B ILE* 4.1 9.6 - - + +
368B HIS* 3.2 10.7 - - - -
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.8 23.1 - - + -
342B THR 3.4 11.7 - - - +
343B THR* 4.7 2.9 - - + -
348B GLU* 1.3 78.1 - - - +
350B ARG* 1.3 67.3 + - - +
362B GLN 4.0 0.2 - - - +
364B ILE* 2.7 53.7 + - + +
366B HIS* 3.8 25.8 - - + +
368B HIS* 3.8 11.4 - - + +
379B ALA* 4.1 13.7 - - + -
388B ILE* 4.5 4.5 - - + -
390B ALA* 3.6 30.5 - - + -
409B TYR* 4.5 11.4 - - + -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 3.1 16.5 + - - +
323B HIS* 3.5 42.0 - - - +
324B GLU* 4.1 5.3 + - - +
340B LEU 3.6 0.3 - - - +
341B LEU* 3.4 8.5 - - - +
342B THR* 2.8 44.8 + - + +
348B GLU* 2.6 39.6 + - + -
349B ILE* 1.3 78.8 - - - +
351B VAL* 1.3 65.4 + - - +
352B TYR* 2.9 39.0 + - + -
360B PRO* 3.5 19.0 - - + +
362B GLN 3.4 3.4 - - - +
363B ILE* 3.6 27.3 - - + +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LYS* 4.2 28.0 - - + +
340B LEU 3.3 3.8 - - - +
341B LEU* 3.9 15.9 - - + -
350B ARG* 1.3 79.4 - - - +
352B TYR* 1.3 63.7 + - - +
360B PRO* 3.8 1.4 - - - +
361B ASP* 2.8 28.2 + - + +
362B GLN* 3.1 31.6 + - + +
364B ILE* 5.1 3.1 - - + -
381B TRP* 3.9 22.9 - - + -
388B ILE* 3.9 16.2 - - + -
411B ALA* 4.3 12.1 - - + +
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Residues in contact with TYR 352 (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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303B VAL* 6.1 0.4 - - + -
321B MET* 3.3 40.5 - - + +
322B PRO* 4.3 0.5 + - - +
323B HIS* 3.7 14.3 - + - -
339B LYS* 3.2 6.4 - - - +
340B LEU* 2.8 43.1 + - + +
342B THR* 4.3 7.9 - - - -
350B ARG* 2.9 52.1 + - + -
351B VAL* 1.3 78.4 - - - +
353B SER* 1.3 61.1 + - - +
357B TRP* 3.5 35.8 - - + -
358B SER 4.0 4.3 - - - -
359B LYS 3.6 13.2 - - - -
360B PRO* 3.4 25.1 - - + +
361B ASP 4.3 1.8 - - - +
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Residues in contact with SER 353 (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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338B THR 3.5 3.5 + - - -
339B LYS* 3.0 25.8 + - - +
352B TYR* 1.3 72.5 - - - +
354B SER* 1.3 60.7 + - - +
355B TYR* 3.3 29.5 - - - -
356B ASP 3.1 30.7 + - - +
357B TRP* 3.3 7.4 + - - -
361B ASP* 2.8 32.1 + - - +
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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