Contacts of the strand formed by residues 198 - 203 (chain H) in PDB entry 1O5F
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 PRO 198 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H TRP* 4.3 15.0 - - + +
30H GLN* 3.4 24.5 - - - +
44H GLY 3.9 2.7 - - - +
45H SER* 3.1 22.6 - - - +
137H THR 4.4 0.2 - - - -
138H VAL* 3.4 29.1 - - - +
139H THR* 3.4 24.0 + - - +
197H GLY* 1.3 85.4 - - - +
199H PHE* 1.3 60.2 + - - +
200H VAL* 3.9 15.0 - - + +
209H LEU* 3.6 15.3 - - + -
213H VAL* 4.7 0.2 - - - -
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Residues in contact with PHE 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H CYS* 3.4 29.4 - - + -
137H THR 3.4 9.0 - - - -
138H VAL* 4.2 5.6 - - + -
160H VAL* 3.8 19.1 - - + -
162H ILE* 3.9 19.3 - - + -
181H PHE* 3.7 24.7 - + - -
183H ALA* 3.7 25.1 - - + -
198H PRO* 1.3 74.3 - - - +
200H VAL* 1.3 58.0 + - - +
201H CYS* 3.7 10.3 - - - -
209H LEU* 3.8 1.7 - - - -
210H CYS* 2.9 28.5 + - + -
211H GLY 3.2 26.6 + - - +
228H TYR* 3.7 30.7 - + + -
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Residues in contact with VAL 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H TRP* 4.0 22.2 - - + -
29H TRP* 3.9 13.9 - - + +
121H VAL* 3.8 23.8 - - + -
136H CYS* 3.2 1.6 - - - +
137H THR* 2.9 39.7 + - + +
139H THR* 5.8 2.5 - - - +
198H PRO* 3.9 16.6 - - + +
199H PHE* 1.3 78.5 - - - +
201H CYS* 1.3 63.6 + - - +
208H ARG* 3.1 39.9 - - + +
209H LEU* 4.0 4.7 - - - -
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Residues in contact with CYS 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H LEU* 5.3 0.2 - - - -
134H LYS* 4.3 15.3 - - + +
135H ILE 5.5 0.4 - - - -
136H CYS* 2.0 48.0 - - - +
162H ILE* 4.3 7.2 - - - -
199H PHE* 3.7 12.3 - - - -
200H VAL* 1.3 72.9 - - - +
202H GLU* 1.3 60.1 + - - +
203H ASP* 4.2 0.9 + - - +
208H ARG* 2.9 37.7 + - - +
210H CYS* 3.6 26.7 - - - -
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Residues in contact with GLU 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H LYS* 3.0 24.1 + - - +
135H ILE 5.9 0.2 + - - -
201H CYS* 1.3 74.7 - - - +
203H ASP* 1.3 64.9 + - - +
208H TRP* 3.2 90.8 + - + +
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Residues in contact with ASP 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H GLN* 2.9 23.1 + - - +
134H LYS* 4.2 10.5 - - - +
201H CYS 5.0 0.7 - - - +
202H GLU* 1.3 77.6 - - - +
204H SER* 1.3 63.5 + - - +
205H ILE* 3.2 27.1 + - + +
206H SER 4.5 0.2 + - - -
208H ARG* 2.8 73.5 - - - +
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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