Contacts of the helix formed by residues 223 - 233 (chain 8) in PDB entry 1O1F
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 223 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2198 VAL* 3.5 22.0 - - + -
2208 ALA* 3.2 39.9 - - + -
2218 LEU 3.5 0.4 - - - -
2228 ASP* 1.3 74.8 - - - +
2248 GLU* 1.4 60.1 + - - +
2268 GLU* 3.6 5.4 - - - +
2278 MET* 3.4 27.9 + - - +
2558 PHE* 3.0 54.1 - + + -
2588 PRO 4.1 0.4 - - - -
2598 GLU* 3.1 49.4 - - + +
2628 PHE* 3.9 2.7 - + - -
3128 ARG* 2.9 39.3 - - - +
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Residues in contact with GLU 224 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2228 ASP* 3.0 17.8 - - - +
2238 PHE* 1.4 76.3 - - - +
2258 ASN* 1.3 82.8 + - - +
2268 GLU 3.1 8.0 + - - -
2278 MET* 3.5 7.1 + - - +
2288 ALA* 3.5 14.6 + - - +
2598 GLU* 4.5 1.1 + - - -
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Residues in contact with ASN 225 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2228 ASP* 3.2 23.3 + - - +
2248 GLU* 1.3 111.6 + - - +
2268 GLU* 1.3 56.1 + - - +
2288 ALA* 3.8 17.6 - - + +
2298 THR* 2.6 23.0 + - - -
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Residues in contact with GLU 226 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2208 ALA* 3.7 22.3 - - + +
2218 LEU 5.1 2.5 - - - +
2228 ASP 3.2 17.5 - - - +
2238 PHE* 3.6 11.4 - - - +
2248 GLU 3.1 0.4 - - - -
2258 ASN* 1.3 78.9 - - - +
2278 MET* 1.3 62.4 + - - +
2288 ALA 3.4 0.4 - - - -
2298 THR* 3.1 23.1 + - - +
2308 ALA* 2.9 21.7 + - - +
2368 LEU* 4.6 7.0 - - - +
2558 PHE* 3.4 37.8 - - + -
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Residues in contact with MET 227 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238 PHE 3.4 15.9 - - - +
2248 GLU* 3.6 8.1 - - - +
2268 GLU* 1.3 75.5 - - - +
2288 ALA* 1.4 57.7 + - - +
2308 ALA* 2.9 29.8 + - - +
2318 ALA* 3.2 8.5 + - - +
2528 ASN* 5.7 1.6 - - - -
2558 PHE* 3.3 21.5 - - + -
2568 ARG* 3.7 30.3 - - + +
2598 GLU* 3.9 17.0 - - - +
2668 PHE* 5.6 4.9 - - + -
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Residues in contact with ALA 228 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248 GLU 3.5 4.2 + - - +
2258 ASN* 3.8 31.2 - - + +
2278 MET* 1.4 77.5 - - - +
2298 THR* 1.3 61.0 + - - +
2318 ALA* 3.4 20.0 + - - +
2328 SER* 3.5 10.8 + - - -
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Residues in contact with THR 229 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258 ASN 2.6 25.1 + - - -
2268 GLU* 3.1 21.6 + - - +
2278 MET 3.2 0.2 - - - -
2288 ALA* 1.3 76.2 - - - +
2308 ALA* 1.3 62.6 + - - +
2318 ALA 3.3 0.5 + - - -
2328 SER* 3.4 10.5 + - - -
2338 SER* 3.3 16.5 + - - -
2348 SER* 4.1 23.0 + - - +
2368 LEU* 4.9 3.6 - - + -
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Residues in contact with ALA 230 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2268 GLU 2.9 14.3 + - - +
2278 MET* 2.9 20.5 + - - +
2298 THR* 1.3 74.0 - - - +
2318 ALA* 1.4 51.9 + - - +
2338 SER* 2.9 32.7 + - - -
2368 LEU* 3.8 16.6 - - + +
2528 ASN* 3.3 36.5 + - + +
2558 PHE* 4.8 1.8 - - + -
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Residues in contact with ALA 231 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2278 MET 3.2 6.2 + - - +
2288 ALA* 3.4 14.6 - - - +
2308 ALA* 1.4 76.0 - - - +
2328 SER* 1.3 61.7 + - - +
2338 SER* 3.0 11.4 + - - -
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Residues in contact with SER 232 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2288 ALA 3.5 9.4 + - - -
2298 THR* 3.4 13.6 + - - -
2318 ALA* 1.3 76.3 - - - +
2338 SER* 1.4 68.4 - - - +
2348 SER* 5.1 1.6 - - - -
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Residues in contact with SER 233 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2298 THR 3.3 1.8 + - - -
2308 ALA 2.9 22.6 + - - -
2318 ALA* 3.0 7.8 + - - -
2328 SER* 1.4 85.0 - - - +
2348 SER* 1.3 69.3 - - - +
2368 LEU* 4.1 3.0 - - - +
2378 GLU* 5.7 4.7 + - - +
2528 ASN* 5.0 2.4 + - - -
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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