Contacts of the strand formed by residues 305 - 310 (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 HIS 305 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B PHE* 3.7 3.8 - - - -
271B GLN* 4.6 2.2 - - - +
301B GLY* 3.2 3.3 - - - -
302B GLY* 2.9 37.2 + - - -
303B GLN 3.8 0.4 - - - -
304B HIS* 1.3 80.8 + - - +
306B THR* 1.3 65.2 + - - +
307B VAL* 4.1 7.0 - - + -
318B LEU 3.5 11.4 - - - +
319B GLY* 4.4 0.7 - - - -
320B ARG 4.1 4.0 - - - +
325B ARG* 3.5 45.9 + - + +
326B LEU* 4.1 3.1 - - + -
352B CYS* 3.4 16.5 - - - -
353B GLY 3.4 24.9 - - - -
354B ALA 3.8 10.5 + - - -
355B SER* 4.1 2.7 - - - -
356B VAL 3.0 29.6 + - - -
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Residues in contact with THR 306 (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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251B PHE* 3.4 18.2 - - - -
253B PHE* 3.7 22.4 - - + -
271B GLN* 2.8 21.0 + - - +
299B PHE* 4.5 8.3 - - + -
300B SER 3.4 13.9 - - - +
301B GLY* 4.2 0.4 - - - -
305B HIS* 1.3 74.9 - - - +
307B VAL* 1.3 73.4 + - - +
308B CYS* 4.7 0.4 - - + +
317B SER* 3.1 6.6 - - - -
318B LEU* 2.9 56.3 + - + +
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Residues in contact with VAL 307 (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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299B PHE 3.6 0.3 - - - -
300B SER* 2.8 46.1 + - - +
305B HIS* 4.1 10.5 - - + -
306B THR* 1.3 77.6 - - - +
308B CYS* 1.3 65.3 + - - +
315B ALA* 5.0 0.7 - - + -
316B TYR 3.2 9.9 - - - +
317B SER* 4.4 8.1 - - - -
341B ILE* 4.4 6.5 - - + -
350B VAL* 3.8 27.2 - - + +
351B ALA 4.8 1.1 - - - +
352B CYS* 3.3 19.3 - - - -
357B GLY* 4.7 2.0 - - - -
358B TYR 4.6 1.3 - - - +
369B TRP* 4.1 33.4 - - + +
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Residues in contact with CYS 308 (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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289B PHE* 3.8 20.9 - - - -
296B TRP* 3.5 24.7 - - + -
298B GLY 3.1 16.2 - - - +
299B PHE* 3.6 18.8 - - + -
306B THR* 4.8 0.4 - - + -
307B VAL* 1.3 75.8 - - - +
309B MET* 1.3 59.8 + - - +
315B ALA* 3.3 5.2 - - - +
316B TYR* 2.7 53.1 + - - -
318B LEU* 4.5 7.6 - - - -
338B PRO* 4.2 3.4 - - - -
350B VAL* 4.3 4.5 - - - -
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Residues in contact with MET 309 (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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296B TRP* 3.6 11.6 - - - -
297B VAL* 3.0 44.0 + - + -
298B GLY* 3.0 21.8 + - - +
308B CYS* 1.3 76.0 - - - +
310B ASP* 1.3 67.2 + - - +
313B GLY* 4.5 3.6 - - - -
314B LYS 3.1 16.4 - - - +
315B ALA* 4.4 0.2 - - - -
347B VAL* 3.3 29.8 - - + +
348B SER* 3.5 12.6 - - - +
349B SER* 3.5 32.8 - - - -
350B VAL* 4.2 12.8 - - + -
362B LYS* 5.0 3.4 - - - +
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Residues in contact with ASP 310 (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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294B LYS* 2.8 42.4 + - + -
295B SER 3.2 15.9 - - - +
296B TRP* 4.2 6.9 - - + +
297B VAL* 3.4 14.2 - - - +
309B MET* 1.3 78.8 - - - +
311B SER* 1.3 61.5 + - - +
312B GLU* 2.8 24.3 + - - +
313B GLY 3.2 7.6 + - - -
314B LYS* 3.0 30.8 + - - +
316B TYR* 3.0 12.7 + - + -
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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