Contacts of the strand formed by residues 356 - 360 (chain D) in PDB entry 2IBS
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 PHE 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D ILE* 3.8 17.7 - - + -
267D ARG 3.6 4.5 - - - -
268D PHE* 3.6 21.1 - + - -
332D VAL* 3.4 8.1 - - - +
333D VAL* 2.9 41.2 + - + +
334D ALA 3.8 8.3 - - - -
335D HIS* 3.4 29.2 - + + -
355D GLU* 1.3 73.6 - - - +
357D HIS* 1.3 63.0 + - - +
358D LEU* 4.0 7.4 - - + -
395D LEU* 3.1 25.6 - - + -
396D THR 3.8 1.3 - - - -
397D LEU* 3.6 36.8 - - + -
400D LEU* 3.6 27.4 - - + -
3E T 4.2 6.3 - - - -
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Residues in contact with HIS 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ARG* 2.7 35.6 + - - +
269D ALA* 3.5 19.9 - - + +
325D PHE* 3.6 26.2 - + + -
326D TYR* 4.1 3.1 - + - -
330D HIS* 2.9 26.6 + - + +
331D LEU 3.7 2.9 - - - -
332D VAL* 3.7 12.6 - - + +
352D TRP* 3.3 46.3 - + + +
354D GLU 3.2 18.6 + - - -
355D GLU 3.2 21.5 + - - -
356D PHE* 1.3 70.7 - - - +
358D LEU* 1.3 62.4 + - - +
359D LEU* 3.4 10.9 - - - +
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.8 26.2 - - + -
264D PHE* 3.6 32.0 - - + -
265D HIS 3.4 3.4 - - - -
266D ILE* 4.0 18.2 - - + -
330D HIS* 3.7 13.7 - - - +
331D LEU* 2.9 43.1 + - + +
333D VAL* 3.8 23.1 - - + -
345D TRP* 5.9 0.2 - - - -
356D PHE* 4.0 19.3 - - + -
357D HIS* 1.3 75.8 - - - +
359D LEU* 1.3 68.3 + - - +
360D PRO* 4.0 4.0 - - - +
400D LEU* 4.0 7.9 - - + -
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D PHE* 3.4 3.0 - - - -
265D HIS* 2.7 56.5 + - + +
267D ARG* 3.9 20.2 - - + -
325D PHE* 3.7 38.6 - - + +
328D THR* 5.3 4.5 - - - +
330D HIS* 3.8 22.2 - - + -
357D HIS 3.4 16.6 - - - +
358D LEU* 1.3 80.4 - - - +
360D PRO* 1.3 73.6 - - + +
361D LYS 3.4 0.2 + - - -
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Residues in contact with PRO 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D LEU 3.7 8.1 - - - +
264D PHE* 3.6 9.2 - - + -
265D HIS* 4.2 4.7 - - - -
330D HIS* 5.6 2.9 - - + -
345D TRP* 5.4 9.6 - - + -
358D LEU 4.0 5.4 - - - +
359D LEU* 1.3 90.2 - - + +
361D LYS* 1.3 68.0 + - - +
364D VAL* 4.6 6.7 - - + +
366D LEU* 3.8 31.6 - - + -
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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