Contacts of the helix formed by residues 28 - 32 (chain B) in PDB entry 1OFD
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 MET 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLY* 3.2 15.7 - - - -
3B VAL 3.0 40.2 - - - +
24B ALA 3.0 19.1 - - - +
25B LEU* 3.0 11.3 + - - +
27B CYS* 1.3 81.7 - - + +
29B GLU* 1.3 54.2 + - - +
30B HIS* 3.2 7.0 - - - -
31B ARG* 2.8 38.2 + - - +
32B GLY 3.7 2.4 + - - -
203B TYR* 3.5 25.1 - - + +
205B ARG* 4.1 12.1 - - + +
366B SER* 3.8 18.4 - - - +
367B GLU* 4.6 11.7 - - - -
370B VAL* 5.0 5.2 - - + -
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Residues in contact with GLU 29 (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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25B LEU 3.6 2.0 + - - -
26B GLY 3.4 16.6 + - - +
27B CYS 3.5 1.2 - - - -
28B MET* 1.3 76.8 - - - +
30B HIS* 1.3 58.3 + - - +
32B GLY* 3.0 24.4 + - - +
34B CYS* 4.2 5.4 - - - -
180B ARG* 3.8 16.4 - - - +
181B SER* 3.0 26.3 + - - +
182B ILE* 5.6 3.5 - - + +
205B ARG* 2.9 42.1 + - - -
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Residues in contact with HIS 30 (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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27B CYS 3.2 27.2 + - - -
28B MET* 4.2 3.8 - - - -
29B GLU* 1.3 78.1 + - - +
31B ARG* 1.3 65.8 + - + +
32B GLY 3.2 6.8 + - - +
207B PHE* 5.0 4.2 - - - -
367B GLU* 2.7 30.3 + - - -
1013B GLU* 4.6 8.0 - - - +
1016B ALA* 5.3 5.0 - - - +
1017B GLN* 4.8 5.8 - - - -
1275B ASN* 3.9 15.3 - - - -
1276B THR* 4.8 8.6 - - - +
1278B ARG* 3.5 53.9 + - - +
1311B GLN* 5.2 2.4 - - + +
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Residues in contact with ARG 31 (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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1B CYS* 2.9 52.9 + - - +
2B GLY* 3.8 6.1 - - - +
28B MET* 2.8 20.3 + - - +
30B HIS* 1.3 91.2 - - + +
32B GLY* 1.3 57.1 + - - +
205B ARG 4.9 0.2 - - - -
207B PHE* 3.5 10.6 - - - +
227B ASN* 4.7 0.6 + - - -
350B ARG* 3.2 29.3 - - - +
351B PRO* 3.9 19.8 - - - +
366B SER* 3.8 22.3 + - - -
367B GLU* 2.9 31.1 + - - +
1013B GLU* 3.8 17.1 - - + +
1014B ASP* 4.4 3.2 + - - -
1311B GLN* 3.0 32.1 - - - +
1331B ASP* 4.5 0.4 + - - -
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Residues in contact with GLY 32 (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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28B MET 3.7 2.6 + - - -
29B GLU* 3.0 18.3 + - - +
30B HIS* 4.1 4.7 - - - +
31B ARG* 1.3 81.2 - - - +
33B GLY* 1.3 59.2 + - - -
205B ARG* 3.9 14.4 - - - -
206B ARG 3.3 16.8 - - - -
207B PHE* 3.5 15.8 - - - -
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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