Contacts of the strand formed by residues 123 - 128 (chain D) in PDB entry 3MA2
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 GLU 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D HIS* 2.5 31.8 - - + +
122D ASN* 1.3 78.8 - - - +
124D ILE* 1.3 57.4 + - - +
125D THR* 4.2 4.3 + - - +
158D ARG* 3.2 18.6 - - + +
160D ARG* 3.2 53.4 + - + +
176D ASP* 4.2 0.3 - - - +
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Residues in contact with ILE 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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119D TRP* 3.5 40.4 - - + -
121D HIS* 3.8 13.5 - - + +
122D ASN 4.2 2.2 - - - +
123D GLU* 1.3 78.6 - - - +
125D THR* 1.3 65.0 + - - +
157D LEU* 3.8 33.9 - - + -
158D ARG 3.0 6.2 + - - +
159D PHE* 3.3 25.7 - - + +
160D ARG 3.0 21.0 + - - -
176D ASP* 3.5 23.6 - - + +
177D ILE* 3.7 24.7 - - + -
245D LEU* 4.1 0.9 - - + -
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Residues in contact with THR 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* 4.5 6.3 - - - +
124D ILE* 1.3 77.0 - - - +
126D PHE* 1.3 63.4 + - - +
160D ARG* 3.2 48.5 - - + +
162D VAL* 4.1 8.3 - - + -
172D GLU* 5.8 0.9 - - - +
174D GLN 4.8 0.2 + - - -
175D ALA* 3.3 12.9 - - - -
176D ASP* 2.7 42.7 + - - +
177D ILE* 2.9 23.9 + - - +
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Residues in contact with PHE 126 (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 THR* 1.3 77.2 - - - +
127D CYS* 1.3 68.1 + - - +
128D ILE* 3.8 22.9 - - + -
145D ARG* 4.5 9.9 - - + -
148D PHE* 3.3 52.7 - + + -
159D PHE* 3.8 26.2 - - + -
160D ARG 3.0 11.9 + - - -
161D GLU* 3.5 48.2 - - + -
162D VAL* 2.8 24.9 + - - -
175D ALA* 3.5 5.3 - - - +
177D ILE* 3.0 16.8 - - + +
179D ILE* 4.2 2.0 - - + -
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Residues in contact with CYS 127 (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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126D PHE* 1.3 78.6 - - - +
128D ILE* 1.3 67.3 + - - +
129D GLN* 3.6 1.4 + - - +
161D GLU* 5.1 0.2 - - - -
162D VAL 3.3 23.1 - - - +
164D TYR* 3.5 42.8 - - - -
167D ILE* 3.9 13.2 - - + -
175D ALA* 3.9 1.3 - - + -
177D ILE 2.9 8.1 + - - -
178D MET* 3.7 20.6 - - - -
179D ILE* 2.9 27.8 + - - +
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Residues in contact with ILE 128 (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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126D PHE* 3.8 28.4 - - + -
127D CYS* 1.3 79.0 - - - +
129D GLN* 1.4 54.9 + - - +
130D ASN 3.4 19.7 - - - +
141D TYR* 2.6 68.2 + - + +
144D ILE* 3.8 42.2 - - + -
145D ARG* 4.7 3.1 - - + -
161D GLU* 4.4 8.1 + - - +
162D VAL 4.5 1.6 + - - -
164D TYR* 4.4 5.0 + - - +
179D ILE* 3.6 18.8 - - + +
180D PHE* 5.9 0.2 - - - -
181D PHE* 5.7 0.2 - - + -
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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