Contacts of the strand formed by residues 299 - 305 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D LEU* 4.6 10.3 - - + -
117D GLU* 5.3 6.9 + - - +
120D ALA* 5.7 0.2 - - - +
121D ILE 3.1 6.8 + - - +
122D THR* 4.2 16.3 + - + -
123D GLU* 2.8 32.7 + - - +
297D SER* 4.0 1.0 - - - -
298D THR* 1.3 79.1 + - - +
300D ARG* 1.3 63.0 + - - +
301D ILE* 4.2 23.6 - - + -
315D ILE* 5.0 11.0 - - + -
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Residues in contact with ARG 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 2.9 47.6 + - - -
125D PHE* 4.1 7.1 - - + -
287D PRO* 3.8 30.3 - - - +
288D ILE 4.9 1.4 + - - -
290D GLY 4.7 2.8 + - - -
293D LEU* 4.2 7.5 - - - +
294D ALA* 3.4 41.5 + - - +
297D SER* 3.7 15.9 - - - +
298D THR 5.5 0.4 - - - -
299D THR* 1.3 78.8 - - - +
301D ILE* 1.3 64.9 + - - +
315D ILE* 3.5 10.9 - - - +
316D TYR* 3.0 55.3 + - + +
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Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PHE* 4.1 16.4 - - + -
111D LEU* 5.0 4.3 - - + -
112D LEU* 3.6 31.0 - - + -
116D ILE* 5.5 1.3 - - + -
122D THR* 3.9 24.9 - - + -
123D GLU 2.7 12.0 + - - +
124D ALA* 3.4 8.6 - - + +
125D PHE* 3.0 31.7 + - - -
265D PHE* 5.9 1.1 - - + -
299D THR* 4.2 8.3 - - + -
300D ARG* 1.3 77.0 - - - +
302D SER* 1.3 76.9 - - - +
303D LEU* 4.0 9.0 - - + -
313D ALA* 3.8 20.4 - - + -
314D LYS 3.4 10.1 - - - +
315D ILE* 5.1 3.4 - - + -
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Residues in contact with SER 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D PHE* 3.6 24.2 - - - -
300D ARG 4.1 0.8 - - - -
301D ILE* 1.3 80.4 - - - +
303D LEU* 1.3 62.9 + - - +
304D ARG* 4.3 13.4 - - - +
313D ALA* 3.4 0.7 - - - -
314D LYS* 2.7 48.5 + - - +
316D TYR* 4.5 9.1 - - - +
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PHE* 4.7 2.9 - - + -
124D ALA* 4.4 11.4 - - + -
125D PHE 2.9 16.9 + - - +
126D GLY* 3.8 15.1 - - - -
127D GLU* 4.9 1.4 + - - +
130D THR* 3.3 28.3 + - + -
131D GLY* 4.0 6.7 - - - +
132D LYS* 3.9 27.8 - - + +
135D LEU* 4.7 8.1 - - + -
270D MET* 5.8 1.2 - - - +
301D ILE* 4.0 10.5 - - + +
302D SER* 1.3 82.9 + - - +
304D ARG* 1.3 66.2 + - - +
312D ILE 3.4 12.3 - - - +
313D ALA* 3.8 16.2 - - + -
328D PHE* 4.0 17.7 - - + -
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Residues in contact with ARG 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLU* 5.9 4.5 - - - +
130D THR* 4.0 7.0 - - - +
302D SER* 4.3 11.7 - - - +
303D LEU* 1.3 79.8 - - - +
305D LYS* 1.3 67.9 + - - +
306D GLY 3.3 0.2 + - - -
311D ARG* 3.5 4.8 - - - -
312D ILE* 2.7 71.3 + - + +
314D LYS* 5.3 5.9 - - - +
325D GLU* 3.6 21.8 + - - -
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Residues in contact with LYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLU* 5.2 4.8 + - - +
129D ARG* 3.4 41.9 - - + +
130D THR* 4.2 5.1 + - - -
304D ARG* 1.3 76.9 + - - +
306D GLY* 1.3 79.1 + - - +
308D GLY 3.3 22.1 + - - +
311D ARG* 3.3 43.3 - - - +
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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