Contacts of the strand formed by residues 217 - 221 (chain A) in PDB entry 1H3F
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 VAL 217 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 3.8 28.5 - - + -
23A VAL 3.8 6.7 - - - +
24A PRO 4.3 2.9 - - - +
27A GLU* 4.0 22.0 - - + +
28A LEU* 3.8 39.5 - - + +
31A LYS* 4.4 7.0 - - + -
189A ASP 2.8 17.9 + - - +
190A VAL* 3.3 14.1 - - + +
191A GLU 3.0 25.5 + - - -
205A ARG* 4.5 1.6 - - - +
216A GLN* 1.3 74.5 - - - +
218A CYS* 1.3 66.1 + - - +
219A PHE* 4.7 1.3 - - + +
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 3.7 2.3 - - - +
22A ILE* 3.4 3.8 - - - -
23A VAL* 2.8 55.7 + - + +
191A GLU 3.9 4.3 - - - -
201A LEU* 3.4 48.5 - - + -
202A LEU* 4.1 6.5 - - + -
205A ARG* 3.7 25.6 - - - -
216A GLN* 4.0 4.9 - - - -
217A VAL* 1.3 76.0 - - - +
219A PHE* 1.3 58.6 + - - +
220A LEU* 3.9 5.5 + - + +
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.3 26.2 - - + -
19A ALA* 3.8 11.9 - - + -
21A GLU 3.9 1.3 - - - -
22A ILE* 3.4 33.4 - - + +
28A LEU* 4.0 13.2 - - + -
61A LYS* 3.8 23.1 - - + -
65A PHE* 3.9 28.3 - + - -
190A VAL* 3.9 9.6 - - + -
191A GLU 3.0 11.5 + - - +
192A MET* 3.5 28.8 - - + +
193A GLY* 3.0 25.8 + - - +
201A LEU* 4.5 0.8 - - - +
217A VAL* 3.7 1.1 + - + -
218A CYS* 1.3 71.1 - - - +
220A LEU* 1.3 64.2 + - - +
221A MET* 3.8 15.9 - - - -
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Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.9 2.4 - - - +
20A GLU* 2.9 22.2 + - + -
21A GLU* 2.9 52.1 + - + +
23A VAL* 5.6 3.6 - - + -
193A GLY 3.2 2.9 - - - +
194A GLY 3.6 16.8 - - - +
195A THR* 4.5 19.7 - - + -
198A ARG* 3.8 35.4 - - + +
201A LEU* 3.5 32.5 - - + -
218A CYS* 4.8 6.7 - - + +
219A PHE* 1.3 74.3 - - - +
221A MET* 1.3 65.2 + - - +
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Residues in contact with MET 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG 5.0 0.2 - - - +
18A GLY* 3.6 24.5 - - - +
19A ALA* 3.8 10.1 - - - -
20A GLU* 3.9 3.6 - - - -
57A VAL* 3.9 33.9 - - + +
58A VAL* 3.9 28.9 - - + -
61A LYS* 4.0 20.6 - - - -
192A MET* 4.1 14.1 - - + -
193A GLY 2.9 6.1 + - - -
194A GLY* 3.4 4.4 - - - -
195A THR 3.1 21.7 + - - -
219A PHE* 3.8 26.7 - - - -
220A LEU* 1.3 74.8 - - - +
222A PRO* 1.3 70.7 - - + +
268A LEU* 5.2 1.8 - - + -
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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