Contacts of the strand formed by residues 353 - 356 (chain B) in PDB entry 3EHN
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 LEU 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.4 46.4 - - + +
52B PRO 3.4 14.8 - - - +
53B ILE* 3.8 23.1 - - + -
66B LEU* 4.9 5.2 - - + -
261B LYS* 3.4 1.6 - - - -
262B ILE* 3.0 43.0 + - + +
272B ASN* 3.9 25.1 - - - +
273B SER* 4.1 2.2 - - - +
274B MET* 4.8 14.6 - - + -
352B PRO* 1.3 76.3 - - + +
354B TYR* 1.3 62.0 + - - +
355B TRP* 3.9 1.9 + - - -
461B PRO* 5.9 6.5 - - + -
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Residues in contact with TYR 354 (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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51B ILE* 3.6 9.0 - - - +
259B GLU* 3.7 13.7 - - - -
260B ALA 3.9 4.0 - - - +
261B LYS* 3.7 21.3 - - + +
352B PRO* 3.2 39.1 - - + +
353B LEU* 1.3 73.5 - - - +
355B TRP* 1.3 61.1 + - - +
356B PHE 4.7 0.2 - - - +
357B ARG* 3.2 70.7 + - + -
461B PRO* 4.5 23.0 - - + +
462B ASN* 3.2 23.8 + - + +
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Residues in contact with TRP 355 (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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47B GLN* 3.1 33.6 + - + -
50B VAL* 3.3 34.1 - - + +
51B ILE* 3.8 24.2 + - + +
142B VAL* 4.2 16.8 - - + -
145B ILE* 3.7 39.8 - - + +
206B ILE* 3.6 41.1 - - + -
214B TRP* 4.5 5.4 - + - -
217B LEU* 4.5 7.0 - - + -
224B ARG* 3.5 17.7 + - - -
260B ALA* 2.9 19.4 + - + +
261B LYS* 5.4 0.2 - - - -
262B ILE* 3.8 15.4 - - + +
353B LEU 4.1 6.5 - - - -
354B TYR* 1.3 78.4 - - - +
356B PHE* 1.3 64.9 + - + +
462B ASN* 3.4 17.5 + - - +
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Residues in contact with PHE 356 (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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145B ILE* 6.3 0.2 - - + -
217B LEU* 3.9 24.0 - - + -
220B SER* 3.2 39.5 - - - -
221B LEU* 4.4 4.9 - - + -
223B LEU* 5.7 0.7 - - + -
224B ARG* 3.3 27.1 - - + +
253B ILE* 4.0 11.6 - - + +
259B GLU* 3.7 1.4 - - - +
260B ALA* 2.7 34.7 + - + +
354B TYR* 3.6 0.4 - - - -
355B TRP* 1.3 80.9 - - - +
357B ARG* 1.3 83.3 + - - +
360B GLU* 3.5 28.0 - - + -
361B THR* 3.4 22.2 - - - -
364B LEU* 3.8 12.8 - - + -
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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