Contacts of the strand formed by residues 120 - 125 (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 ALA 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C ASN* 4.2 1.1 - - - +
95D ARG* 6.2 0.2 - - - +
117D GLU* 3.7 31.7 - - + +
118D SER 3.3 3.8 - - - +
119D MET* 1.3 82.4 - - - +
121D ILE* 1.3 63.8 + - - +
122D THR* 3.9 3.3 + - - +
257D SER* 3.0 16.9 + - - -
264D VAL* 3.3 22.0 + - - +
298D THR* 3.7 23.3 - - + +
299D THR* 5.6 3.4 - - - +
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Residues in contact with ILE 121 (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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120D ALA* 1.3 77.0 - - - +
122D THR* 1.3 64.1 + - - +
250D LEU* 4.3 5.2 - - + +
253D LEU* 3.6 28.3 - - + -
254D GLN* 3.6 33.2 - - + +
257D SER* 4.2 3.6 - - - +
264D VAL* 3.4 29.4 - - + +
266D VAL* 4.2 23.1 - - + -
293D LEU* 6.3 0.4 - - + -
296D ALA* 3.9 18.8 - - + +
297D SER* 3.7 12.7 - - - +
298D THR* 2.7 35.6 + - + +
299D THR 3.1 8.7 + - - +
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Residues in contact with THR 122 (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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112D LEU* 5.3 2.5 - - + -
116D ILE* 3.8 40.7 - - + +
117D GLU* 4.1 13.0 + - - +
120D ALA* 3.9 3.5 + - - +
121D ILE* 1.3 75.2 - - - +
123D GLU* 1.3 61.2 + - - +
264D VAL 2.9 7.7 + - - -
265D PHE* 3.3 12.1 - - + -
266D VAL* 2.8 25.3 + - - +
299D THR* 3.4 19.3 + - + +
301D ILE* 3.9 27.6 - - + -
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Residues in contact with GLU 123 (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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121D ILE 3.8 0.8 + - - -
122D THR* 1.3 74.6 - - - +
124D ALA* 1.3 58.8 + - - +
125D PHE* 3.1 20.4 - - + -
266D VAL* 3.4 20.4 - - + +
268D ASN* 3.8 13.7 - - + +
287D PRO* 4.3 0.2 - - - +
293D LEU* 3.5 21.0 - - + +
297D SER* 2.8 27.0 + - - +
299D THR 2.8 13.2 + - - +
300D ARG* 2.9 42.3 + - - -
301D ILE* 2.7 34.7 + - - +
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Residues in contact with ALA 124 (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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122D THR 4.1 0.2 + - - -
123D GLU* 1.3 75.8 - - - +
125D PHE* 1.3 60.9 + - - +
132D LYS* 4.0 6.5 - - + +
135D LEU* 4.5 3.6 - - + -
265D PHE* 3.8 28.3 - - + -
266D VAL 2.8 10.1 + - - -
267D THR* 3.1 9.2 - - - -
268D ASN* 2.9 22.2 + - - +
301D ILE* 3.4 17.0 - - + +
303D LEU* 4.4 19.1 - - + -
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Residues in contact with PHE 125 (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* 3.1 26.0 - - + -
124D ALA* 1.3 74.5 - - - +
126D GLY* 1.3 53.7 + - - +
132D LYS* 4.1 4.5 - - - +
268D ASN* 3.5 28.9 - - + +
269D GLN 4.5 3.1 - - - +
270D MET* 3.6 23.6 - - + -
287D PRO* 3.8 27.8 - - + -
300D ARG* 4.1 14.6 - - + -
301D ILE 3.0 14.9 + - - +
302D SER* 4.2 16.4 - - - -
303D LEU* 2.9 36.0 + - - +
316D TYR* 3.5 42.6 - + + -
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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