Contacts of the helix formed by residues 298 - 309 (chain B) in PDB entry 2I91
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 SER 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B ALA* 2.5 34.6 + - - -
296B PRO 3.0 5.2 + - - -
297B ALA* 1.3 85.1 - - - +
299B SER* 1.3 64.2 + - - +
300B GLU* 3.8 17.1 + - - +
301B VAL* 3.1 23.8 + - - +
302B SER* 3.3 20.1 + - - -
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Residues in contact with SER 299 (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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298B SER* 1.3 73.4 - - - +
300B GLU* 1.3 68.8 + - - +
302B SER* 2.9 12.2 + - - -
303B SER* 2.8 27.5 + - - -
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Residues in contact with GLU 300 (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 LYS* 3.0 37.8 + - + +
273B LEU* 3.5 23.7 - - + +
293B VAL* 2.9 25.5 - - + +
294B LEU* 3.7 3.1 - - + -
298B SER* 3.9 15.5 - - - +
299B SER* 1.3 87.4 + - - +
301B VAL* 1.3 59.6 + - - +
303B SER* 3.1 9.7 + - - -
304B VAL* 2.9 25.6 + - - +
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Residues in contact with VAL 301 (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 LEU* 3.4 43.3 - - + +
295B ALA 3.4 6.5 - - - +
297B ALA* 5.3 4.0 - - - +
298B SER* 3.1 25.2 + - - +
300B GLU* 1.3 75.6 - - - +
302B SER* 1.3 66.0 + - - +
304B VAL* 3.1 13.0 + - - +
305B CYS* 3.1 13.5 + - - -
346B ASP* 3.7 22.7 - - - +
348B SER* 4.2 11.4 - - - -
349B ILE* 3.6 21.5 - - + -
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Residues in contact with SER 302 (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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297B ALA 5.6 0.2 - - - -
298B SER 3.3 10.4 + - - -
299B SER* 2.9 13.8 + - - -
301B VAL* 1.3 80.8 - - - +
303B SER* 1.3 63.2 + - - +
305B CYS* 3.6 6.7 + - - +
306B GLU* 3.2 32.9 + - - +
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Residues in contact with SER 303 (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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273B LEU* 5.7 3.6 - - - -
274B GLN 5.6 2.3 + - - -
299B SER 2.8 11.9 + - - -
300B GLU* 3.2 14.4 - - - -
301B VAL 3.1 0.2 - - - -
302B SER* 1.3 76.9 - - - +
304B VAL* 1.3 64.3 + - - +
306B GLU* 3.0 17.2 + - - +
307B ARG* 3.1 27.7 + - - +
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Residues in contact with VAL 304 (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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273B LEU* 3.9 12.8 - - + -
281B LEU* 3.8 27.8 - - + -
285B LEU* 3.8 15.7 - - + -
294B LEU* 3.7 20.6 - - + -
300B GLU 2.9 17.3 + - - +
301B VAL 3.1 8.0 + - - +
303B SER* 1.3 75.2 - - - +
305B CYS* 1.3 65.9 + - - +
307B ARG* 2.9 15.2 + - - +
308B LEU* 2.9 38.6 + - + +
349B ILE* 3.9 12.6 - - + -
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Residues in contact with CYS 305 (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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301B VAL* 3.1 11.7 + - - -
302B SER* 3.8 8.3 - - - +
304B VAL* 1.3 79.1 - - - +
306B GLU* 1.3 60.4 + - - +
308B LEU* 3.5 1.2 + - - +
309B THR* 2.9 32.8 + - - +
348B SER* 3.5 34.5 - - - -
349B ILE* 3.4 28.3 - - - -
352B ALA* 3.8 16.8 - - + -
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Residues in contact with GLU 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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302B SER* 3.2 20.4 + - - +
303B SER* 3.0 12.4 + - - +
305B CYS* 1.3 80.6 - - - +
307B ARG* 1.3 61.7 + - + +
309B THR* 3.7 10.9 + - - -
310B ASN* 3.8 15.1 + - - +
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Residues in contact with ARG 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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273B LEU* 3.9 10.7 + - - +
274B GLN 4.4 4.6 + - - -
275B ASP* 4.0 7.5 + - - +
276B MET* 2.7 42.2 + - - +
277B PRO* 4.5 1.2 - - - +
278B LEU* 3.6 45.7 - - + +
281B LEU* 4.0 17.1 - - + +
303B SER* 3.1 23.8 + - - +
304B VAL* 2.9 7.6 + - - +
306B GLU* 1.3 76.5 - - + +
308B LEU* 1.3 64.7 + - - +
309B THR 3.1 3.0 + - - -
310B ASN* 3.1 22.6 + - - +
313B LEU* 4.9 16.2 - - + +
314B LEU* 4.6 0.3 - - - +
14F A 5.5 2.2 + - - -
15F A 6.0 0.2 + - - -
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Residues in contact with LEU 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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278B LEU* 4.8 8.1 - - + +
281B LEU* 4.5 17.9 - - + -
282B LEU* 3.8 28.7 - - + -
285B LEU* 4.2 8.7 - - + -
304B VAL* 2.9 39.8 + - + +
305B CYS* 4.1 4.0 - - - +
307B ARG* 1.3 76.3 - - - +
309B THR* 1.3 61.2 + - + +
310B ASN 3.4 0.7 - - - -
314B LEU* 3.1 23.5 - - + +
324B ILE* 5.8 0.9 - - + -
349B ILE* 4.6 4.9 - - + -
352B ALA* 4.6 9.6 - - + +
353B LEU* 3.8 22.9 - - + -
356B ALA* 2.9 29.8 - - + +
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Residues in contact with THR 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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305B CYS 2.9 22.2 + - - +
306B GLU* 3.7 8.1 + - - +
307B ARG 3.1 0.4 - - - -
308B LEU* 1.3 76.4 - - - +
310B ASN* 1.3 58.7 + - - +
311B GLU 3.4 1.7 + - - -
314B LEU* 4.5 0.4 - - - -
352B ALA* 3.3 37.5 - - + +
355B ASN* 4.1 13.7 - - + +
356B ALA* 4.4 1.8 - - - +
359B LYS* 3.3 39.5 + - - +
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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