Contacts of the strand formed by residues 125 - 131 (chain D) in PDB entry 3IML
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 LEU 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C THR* 3.6 17.5 - - + +
9C SER* 3.8 16.4 - - - +
10C GLU* 3.5 35.0 + - + +
171C GLN* 4.4 5.4 - - - +
251C ILE* 4.8 0.7 - - + -
256C GLY* 3.5 29.4 - - - +
257C GLY* 4.6 2.2 - - - -
124D GLY* 1.3 78.3 - - - -
126D MET* 1.3 72.8 + - - +
127D PHE* 5.6 4.0 - - + -
262D GLY* 3.2 47.7 - - - +
263D GLY 4.0 1.4 + - - -
264D GLY 5.2 0.2 + - - -
275D ASP* 4.6 1.2 + - - +
302D VAL 3.6 8.5 - - - +
303D SER* 4.1 6.1 - - - +
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Residues in contact with MET 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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124D GLY* 4.0 1.8 - - - -
125D LEU* 1.3 105.4 - - - +
127D PHE* 1.3 64.6 + - - +
261D HIS* 6.5 0.9 - - + -
262D GLY* 4.2 8.7 - - - +
263D GLY 5.8 0.9 - - - +
264D GLY 5.9 0.2 - - - +
274D VAL* 3.3 34.1 - - + +
275D ASP* 2.9 40.2 - - - +
278D ALA* 3.5 24.9 - - + +
279D ALA* 4.3 16.6 - - + +
301D GLN* 3.8 0.7 - - - +
302D VAL* 2.7 46.7 + - + +
304D TYR* 3.6 17.3 - - + -
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Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PHE* 4.1 14.4 - + - -
257C GLY* 3.5 25.1 - - - -
125D LEU* 5.6 3.6 - - + -
126D MET* 1.3 79.3 - - - +
128D GLY* 1.3 59.7 + - - +
255D TYR* 4.4 10.1 - - + -
259D ALA* 5.6 0.7 - - + -
260D PRO* 3.5 46.2 - - + +
261D HIS* 3.9 3.1 - - - -
262D GLY* 3.7 25.6 - - - +
278D ALA 5.7 0.4 - - - -
279D ALA* 4.3 19.7 - - - +
282D GLY* 4.8 3.8 - - - -
299D LEU* 4.5 17.3 - - + -
300D ILE 3.4 8.7 - - - +
301D GLN* 3.6 39.5 - - + -
364D PHE* 5.9 0.2 - - - -
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D PHE* 1.3 73.5 - - - +
129D TYR* 1.3 60.1 + - - -
255D TYR* 3.7 6.7 - - - -
282D GLY* 3.6 29.7 - - - -
286D ALA* 4.3 1.3 - - - -
299D LEU* 3.0 10.3 - - - +
300D ILE* 2.8 36.2 + - - +
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Residues in contact with TYR 129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D GLY* 1.3 74.4 - - - +
130D ALA* 1.3 74.6 + - - +
131D CYS* 3.7 14.7 - - + +
133D GLU* 4.8 3.6 + - - -
139D PRO* 3.8 31.3 - - + +
255D TYR* 3.1 38.4 + + + -
258D ALA* 4.5 16.5 + - + +
259D ALA* 3.7 25.4 - - + -
282D GLY 4.2 0.2 + - - -
283D ARG* 3.3 12.0 + - - -
286D ALA* 3.6 6.3 - - - +
297D ARG* 3.6 37.6 + - - -
298D ALA 3.4 19.1 - - - -
299D LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D TYR* 1.3 82.9 - - - +
131D CYS* 1.3 64.1 + - - +
137D LEU* 3.6 8.5 - - + +
139D PRO* 5.5 0.4 - - - -
283D ARG* 3.3 18.2 - - - +
286D ALA* 3.6 30.3 - - + +
287D LYS* 3.6 5.2 - - - +
290D VAL* 4.0 8.3 - - + -
297D ARG* 3.6 0.7 - - - +
298D ALA 2.8 31.9 + - - +
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Residues in contact with CYS 131 (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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129D TYR* 3.7 13.2 - - + +
130D ALA* 1.3 78.9 - - - +
132D ASP* 1.3 59.8 + - - +
133D GLU* 3.1 31.1 + - + +
137D LEU* 3.1 33.1 + - - +
138D MET 3.7 0.4 - - - -
139D PRO* 3.5 36.6 - - - -
290D VAL* 4.2 6.7 - - - +
296D SER 3.4 8.1 - - - -
297D ARG* 3.3 17.9 - - + +
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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