Contacts of the helix formed by residues 290 - 298 (chain B) in PDB entry 4I5L
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 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B SER* 1.3 73.3 - - - +
291B PHE* 1.3 62.9 + - - +
293B GLN* 3.2 21.9 - - - +
294B ASN* 2.8 32.7 + - - -
309B GLU* 2.5 34.3 + - - -
310B PHE* 3.8 6.0 - - - -
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Residues in contact with PHE 291 (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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217B PHE* 4.0 21.8 - + - -
234B PHE* 4.0 8.7 - + - -
237B PHE* 3.9 14.6 - + - -
269B ILE* 3.5 46.0 - - + -
273B VAL* 4.1 9.4 - - + -
286B LEU* 3.8 21.8 - - + -
289B SER* 3.1 15.8 + - - +
290B SER* 1.3 79.5 + - - +
292B LEU* 1.3 64.8 + - + +
294B ASN* 3.2 5.2 + - - +
295B VAL* 3.0 46.6 + - + +
310B PHE* 3.8 22.5 - + + -
311B PHE* 3.8 17.3 - + - -
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Residues in contact with LEU 292 (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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175B PRO* 5.7 0.5 - - - +
178B TRP* 4.4 9.8 + - + +
213B ASP* 3.7 17.9 - - + +
214B ALA* 3.5 40.4 - - + +
217B PHE* 3.9 35.0 - - + -
286B LEU* 4.3 16.5 + - + +
289B SER 5.2 0.2 + - - -
290B SER 3.4 0.4 - - - -
291B PHE* 1.3 87.0 - - + +
293B GLN* 1.3 72.8 + - - +
295B VAL* 3.1 10.2 + - + +
296B ALA* 3.0 22.3 + - - +
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Residues in contact with GLN 293 (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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287B ARG 5.7 1.2 + - - -
289B SER 3.6 10.4 + - - +
290B SER* 3.2 32.7 - - - +
292B LEU* 1.3 79.0 + - - +
294B ASN* 1.3 60.1 + - - +
296B ALA* 3.2 10.4 + - - +
297B LEU* 3.0 36.5 + - + +
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Residues in contact with ASN 294 (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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290B SER* 2.8 29.1 + - - -
291B PHE 3.4 9.0 - - - +
292B LEU 3.2 0.6 - - - -
293B GLN* 1.3 78.2 - - - +
295B VAL* 1.3 65.6 + - - +
297B LEU* 3.1 22.5 + - - +
298B LEU* 3.2 16.1 + - - +
307B LEU* 4.1 26.0 - - - +
309B GLU* 3.1 36.3 + - - +
310B PHE* 3.7 15.4 + - + -
311B PHE* 4.0 16.6 - - + -
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Residues in contact with VAL 295 (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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175B PRO* 4.8 1.8 - - + +
177B TYR* 4.1 13.1 - - + +
178B TRP* 3.7 33.2 - - + +
217B PHE* 4.8 3.4 - - + -
237B PHE* 4.0 26.9 - - + -
291B PHE* 3.0 46.7 + - + +
292B LEU* 3.1 14.6 + - + +
294B ASN* 1.3 73.9 - - - +
296B ALA* 1.3 63.2 + - - +
298B LEU* 3.3 26.2 + - - +
299B GLU* 4.5 0.7 + - - +
311B PHE* 4.3 1.3 - - + -
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Residues in contact with ALA 296 (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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175B PRO* 4.1 26.7 - - + +
292B LEU 3.0 11.0 + - - +
293B GLN* 3.4 12.8 - - - +
294B ASN 3.1 0.2 - - - -
295B VAL* 1.3 78.1 - - - +
297B LEU* 1.3 61.8 + - + +
298B LEU 3.3 0.3 + - - -
299B GLU* 3.2 25.6 - - - +
300B GLU* 3.5 7.4 - - - +
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Residues in contact with LEU 297 (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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293B GLN* 3.0 26.5 + - + +
294B ASN* 3.1 15.1 + - - +
296B ALA* 1.3 75.6 - - - +
298B LEU* 1.3 63.8 + - - +
299B GLU 3.2 0.4 - - - -
300B GLU* 2.9 32.5 + - + +
301B GLU* 3.0 17.2 + - + +
307B LEU* 4.0 25.6 - - + -
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Residues in contact with LEU 298 (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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177B TYR* 3.4 31.3 - - + -
237B PHE* 4.2 8.1 - - + -
241B VAL* 4.2 12.6 - - + -
245B HIS* 3.0 32.9 + - + -
294B ASN 3.2 12.7 + - - +
295B VAL* 3.3 26.7 - - - +
296B ALA 3.2 1.0 - - - -
297B LEU* 1.3 76.3 - - - +
299B GLU* 1.3 59.0 + - - +
301B GLU 3.2 9.7 - - - +
304B ILE* 3.7 30.5 - - + -
307B LEU* 3.9 14.8 - - + +
311B PHE* 4.0 24.0 - - + -
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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