Contacts of the strand formed by residues 299 - 304 (chain C) in PDB entry 5H1C
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 ARG 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B PHE* 4.5 15.3 - - - -
124C GLU* 2.5 61.5 + - - +
126C PHE* 2.7 44.0 - - + -
286C PRO* 3.7 6.1 - - - +
292C ILE* 3.9 1.0 + - - +
293C ALA* 3.1 37.2 + - - +
296C SER* 3.1 10.3 + - - -
298C THR* 1.3 76.6 - - - +
300C LEU* 1.3 77.2 + - - +
314C ILE* 3.6 2.6 - - - +
315C TYR* 2.9 64.6 + - + +
316C ASP* 4.0 7.3 + - + -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C LEU* 6.4 0.2 - - + -
113C LEU* 4.0 35.2 - - + -
117C ILE* 5.6 7.0 - - + -
123C THR* 5.8 4.0 - - - -
124C GLU 2.9 22.4 + - - +
125C MET* 4.5 20.0 - - + -
126C PHE* 2.8 39.7 + - - +
136C ILE* 6.6 0.2 - - + -
298C THR* 5.7 3.4 - - - +
299C ARG* 1.3 87.7 - - - +
301C TYR* 1.3 54.8 + - - +
302C LEU* 5.3 4.9 - - + -
312C CYS* 3.6 29.2 - - - -
313C GLN 3.5 2.9 - - - -
314C ILE* 4.0 16.6 - - + -
315C TYR* 4.6 0.7 - - - -
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Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.3 33.2 - + + -
127C GLY* 5.1 3.6 - - - -
269C VAL* 6.1 1.8 - - + -
282C ASP 4.7 6.6 + - - -
284C LYS* 3.7 41.1 + - + +
300C LEU* 1.3 76.3 - - - +
302C LEU* 1.3 68.6 + - - +
303C ARG* 3.4 38.4 - - + +
311C ILE 3.3 3.3 - - - +
312C CYS* 3.3 2.9 - - - -
313C GLN* 2.8 65.3 + - + +
315C TYR* 3.5 27.6 - + + -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C MET* 4.8 13.0 - - + -
126C PHE 2.6 21.6 + - - +
127C GLY* 4.0 3.1 - - - -
128C GLU 4.8 0.3 + - - -
131C THR* 3.1 46.8 - - - +
133C LYS* 4.2 22.0 - - + -
136C ILE* 4.2 17.7 - - + -
300C LEU* 5.2 3.6 - - + -
301C TYR* 1.3 91.1 - - - +
303C ARG* 1.3 60.8 + - - +
310C ARG* 5.9 1.8 - - + -
311C ILE 3.2 3.8 - - - +
312C CYS* 3.6 31.2 - - + +
327C PHE* 4.4 13.2 - - + -
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C THR* 5.0 0.7 - - - -
301C TYR* 3.4 34.7 - - + +
302C LEU* 1.3 74.5 - - - +
304C LYS* 1.3 66.8 + - - +
310C ARG* 3.7 2.0 - - - -
311C ILE* 2.8 66.6 + - + +
313C GLN* 3.7 19.2 - - - +
324C GLU* 3.3 25.1 + - - -
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE 5.7 0.2 - - - +
130C ARG* 1.7 64.7 - - + +
131C THR* 4.7 6.9 - - + +
302C LEU 4.0 1.6 + - - -
303C ARG* 1.3 77.6 - - - +
305C GLY* 1.3 78.7 + - - +
307C GLY 4.6 6.3 - - - +
310C ARG* 3.5 33.0 - - - +
311C ILE* 5.2 2.0 - - - +
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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