Contacts of the strand formed by residues 299 - 305 (chain A) in PDB entry 4HYY
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 THR 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU* 4.1 26.5 - - + -
117A GLU* 6.2 0.3 - - - +
121A ILE 3.5 4.4 + - - +
122A THR* 3.3 21.1 + - + -
123A GLU 2.9 24.4 + - - -
297A SER* 3.9 2.1 - - - -
298A THR* 1.3 86.1 + - - +
300A ARG* 1.3 66.1 + - - +
301A ILE* 4.3 5.8 - - + -
315A ILE* 5.0 11.0 - - + -
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Residues in contact with ARG 300 (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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123A GLU* 2.6 57.3 + - - +
125A PHE* 4.0 12.8 - - + -
287A PRO* 3.6 30.8 + - - +
288A ILE 4.5 2.4 + - - -
290A GLY 4.6 3.6 + - - -
293A LEU* 4.3 6.3 - - - +
294A ALA* 3.3 43.9 + - - +
297A SER* 3.8 18.6 - - - +
298A THR 5.5 0.2 - - - -
299A THR* 1.3 79.1 - - - +
301A ILE* 1.3 58.9 + - - +
315A ILE* 3.5 9.3 - - - +
316A TYR* 2.8 53.0 + - + +
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Residues in contact with ILE 301 (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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108A PHE* 3.7 17.0 - - + -
111A LEU* 5.3 0.9 - - + -
112A LEU* 3.5 34.8 - - + -
116A ILE* 5.0 2.5 - - + -
122A THR* 3.8 21.3 - - + -
123A GLU 2.7 11.8 + - - +
124A ALA* 3.4 10.1 - - + +
125A PHE* 2.9 32.4 + - - +
135A LEU* 5.5 1.8 - - + -
265A PHE* 5.7 0.2 - - + -
299A THR* 4.5 4.9 - - + -
300A ARG* 1.3 76.0 - - - +
302A SER* 1.3 73.3 + - - +
303A LEU* 3.9 10.7 - - + +
313A ALA* 3.8 21.3 - - + -
314A LYS 3.2 10.8 - - - +
315A ILE* 5.4 3.6 - - + -
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Residues in contact with SER 302 (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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125A PHE* 3.4 28.9 + - - -
270A MET* 5.5 3.5 - - - +
300A ARG 4.2 0.8 - - - -
301A ILE* 1.3 75.0 - - - +
303A LEU* 1.3 69.5 + - - +
304A ARG* 5.2 7.2 + - - +
312A ILE 3.7 0.7 - - - +
313A ALA* 3.4 4.7 - - - -
314A LYS* 2.6 49.8 + - - +
316A TYR* 4.4 8.2 - - - +
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Residues in contact with LEU 303 (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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108A PHE* 4.3 5.6 - - + -
124A ALA* 4.0 20.2 - - + -
125A PHE 2.9 12.1 + - - +
126A GLY* 3.4 16.7 - - - -
127A GLU* 3.9 2.4 + - - +
130A THR* 2.9 28.9 + - + -
131A GLY* 4.1 5.4 - - - +
132A LYS* 3.9 25.8 - - + +
135A LEU* 5.2 5.2 - - + -
270A MET* 5.1 3.5 - - - +
301A ILE* 3.9 12.8 - - + +
302A SER* 1.3 86.9 + - - +
304A ARG* 1.3 62.1 + - - +
312A ILE 3.4 2.7 - - - -
313A ALA* 3.7 23.3 - - + -
328A PHE* 3.9 19.5 - - + -
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Residues in contact with ARG 304 (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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127A GLU* 5.6 6.7 - - + +
130A THR* 3.6 9.8 - - - +
302A SER* 5.2 6.6 + - - +
303A LEU* 1.3 77.5 - - - +
305A LYS* 1.3 59.5 + - - +
311A ARG* 3.4 8.0 - - - +
312A ILE* 2.6 68.5 + - + +
314A LYS* 4.4 14.6 - - - +
325A GLU* 3.5 30.9 + - - -
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Residues in contact with LYS 305 (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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127A GLU* 4.5 16.8 - - - +
128A PHE 5.2 1.1 - - - +
129A ARG* 4.6 19.1 - - + +
130A THR* 5.2 1.8 - - - +
304A ARG* 1.3 82.5 + - - +
306A GLY* 1.3 67.7 + - - +
308A GLY* 4.4 11.8 + - - -
310A LEU 3.6 4.3 - - - +
311A ARG* 3.7 40.6 - - - +
312A ILE* 4.7 3.7 - - - +
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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