Contacts of the strand formed by residues 315 - 319 (chain B) in PDB entry 1I2M
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 ALA 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B VAL* 5.0 1.1 - - + -
308B CYS 3.3 8.3 - - - +
309B MET* 4.3 0.9 - - + +
313B GLY 4.0 0.8 + - - -
314B LYS* 1.3 73.2 - - - +
316B TYR* 1.3 67.4 + - - +
340B LEU* 3.6 5.0 - - - +
341B ILE* 2.9 35.8 + - + +
344B LEU* 3.9 28.4 - - + +
347B VAL* 4.3 8.9 - - + +
350B VAL* 4.2 19.1 - - + -
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Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS* 2.7 37.7 + - - -
296B TRP* 3.5 27.6 - + - -
307B VAL* 3.2 5.4 - - - +
308B CYS* 2.7 44.9 + - - -
310B ASP* 3.0 17.6 + - - -
314B LYS* 3.5 30.5 - - + +
315B ALA* 1.3 77.0 - - - +
317B SER* 1.3 61.4 + - - +
338B PRO* 3.9 26.5 - - + -
339B THR 3.2 8.3 - - - +
340B LEU* 3.4 39.7 - - + +
341B ILE* 4.0 4.0 - - - -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B THR 3.1 11.2 - - - -
307B VAL* 4.4 7.2 - - - -
316B TYR* 1.3 75.8 - - - +
318B LEU* 1.3 65.2 + - - +
326B LEU* 2.8 48.2 + - - +
328B LEU* 3.8 11.3 - - - +
335B LYS* 4.5 1.4 - - - +
339B THR* 2.9 33.3 + - - -
341B ILE* 4.0 7.1 - - - +
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Residues in contact with LEU 318 (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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270B HIS 3.5 20.2 - - - +
271B GLN 3.9 5.6 - - - +
273B GLY* 3.8 20.2 - - - +
289B PHE* 4.0 24.9 - - + -
305B HIS* 3.5 2.6 - - - -
306B THR* 2.9 62.3 + - + +
308B CYS* 4.5 4.5 - - - -
317B SER* 1.3 81.2 - - - +
319B GLY* 1.3 60.6 + - - +
326B LEU* 3.6 7.3 - - - +
335B LYS* 3.8 12.3 - - - +
336B SER 4.3 3.1 - - - +
337B ILE 3.6 13.5 - - - +
338B PRO* 4.2 16.2 - - + -
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Residues in contact with GLY 319 (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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269B TYR 3.1 22.7 - - - -
270B HIS 4.3 5.8 + - - -
271B GLN 4.5 0.7 - - - -
304B HIS 3.7 6.3 - - - -
305B HIS* 4.4 0.7 - - - -
318B LEU* 1.3 75.3 - - - +
320B ARG* 1.3 66.2 + - - -
326B LEU* 3.6 4.2 - - - +
334B GLU* 3.3 5.4 - - - +
335B LYS 2.8 34.1 + - - -
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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