Contacts of the strand formed by residues 124 - 131 (chain C) 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 GLY 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C GLN* 1.3 74.8 - - - +
125C LEU* 1.3 60.4 + - - -
126C MET* 3.8 15.8 - - - +
275C ASP* 4.9 3.4 - - - -
303C SER* 3.3 5.5 + - - -
304C TYR* 2.9 27.9 + - - +
10D GLU* 3.2 16.2 - - - -
171D GLN* 3.0 13.3 + - - -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLY* 1.3 74.8 - - - +
126C MET* 1.3 69.2 + - - +
127C PHE* 4.6 0.2 - - + -
262C GLY* 3.1 46.3 - - - +
263C GLY 4.1 0.2 + - - -
264C GLY 5.3 0.2 + - - -
275C ASP* 4.8 2.3 - - - +
301C GLN* 3.3 17.5 - - - +
302C VAL 3.4 11.7 - - - +
303C SER* 4.6 5.4 - - - +
8D THR* 3.0 26.7 - - + +
9D SER* 4.2 2.5 - - - -
10D GLU* 3.8 40.1 - - + +
171D GLN* 5.2 0.9 - - - +
251D ILE* 5.6 1.1 - - + -
256D GLY* 3.3 25.1 - - - +
257D GLY* 4.4 2.5 - - - -
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Residues in contact with MET 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLY* 4.1 11.2 - - - -
125C LEU* 1.3 81.8 - - - +
127C PHE* 1.3 63.9 + - - +
261C HIS* 6.3 2.9 - - + -
262C GLY* 4.2 6.7 - - - +
263C GLY 5.9 0.2 - - - +
274C VAL* 3.3 19.5 - - + +
275C ASP* 3.1 50.9 - - - +
278C ALA* 3.4 23.6 - - + -
279C ALA* 4.1 17.7 - - + +
282C GLY* 6.1 0.3 - - - -
300C ILE 3.9 0.5 - - - +
301C GLN* 3.8 1.8 - - - +
302C VAL* 3.1 43.1 + - + +
304C TYR* 3.8 24.5 - - - -
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Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU* 4.6 0.2 - - + -
126C MET* 1.3 76.4 - - - +
128C GLY* 1.3 57.6 + - - +
254C THR* 6.0 0.9 - - - +
255C TYR* 4.0 14.1 - - + -
259C ALA* 5.5 1.6 - - + -
260C PRO* 3.2 39.0 - - + +
261C HIS* 4.1 4.3 - - - -
262C GLY* 3.6 20.4 - - - +
279C ALA* 4.4 16.2 - - - +
282C GLY* 5.0 3.1 - - - -
299C LEU* 3.8 22.0 - - + -
300C ILE 3.1 15.7 - - - -
301C GLN* 3.3 46.0 - - + -
315C MET* 5.3 4.3 - - - -
364C PHE* 5.3 0.7 - - - -
7D PHE* 3.9 6.1 - + - -
257D GLY* 3.5 34.3 - - - -
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C MET 4.3 0.2 + - - -
127C PHE* 1.3 73.7 - - - +
129C TYR* 1.3 62.6 + - - +
255C TYR* 3.9 3.6 - - - -
282C GLY* 3.4 32.1 - - - -
286C ALA* 4.0 2.0 - - - -
299C LEU* 3.3 7.2 - - - +
300C ILE* 2.7 42.6 + - - +
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLY* 1.3 74.2 - - - -
130C ALA* 1.3 85.3 + - - +
131C CYS* 4.1 12.3 - - + +
139C PRO* 4.0 31.6 - - + +
255C TYR* 3.2 33.7 + + + -
258C ALA* 4.2 21.1 + - + +
259C ALA* 3.7 26.2 - - + -
282C GLY 4.1 0.2 + - - -
283C ARG* 3.0 20.6 + - - -
286C ALA* 3.5 7.2 - - - +
297C ARG* 3.4 35.1 + - + -
298C ALA 3.3 17.9 - - - -
299C LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C TYR* 1.3 89.5 - - - +
131C CYS* 1.3 64.9 + - - +
137C LEU* 3.7 9.4 - - + +
139C PRO* 5.3 0.4 - - - -
283C ARG* 3.5 12.3 - - - +
286C ALA* 3.4 33.0 - - + +
287C LYS* 3.6 5.8 - - - +
290C VAL* 4.1 7.4 - - + -
297C ARG* 3.5 0.5 - - - -
298C ALA 3.0 28.2 + - - +
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Residues in contact with CYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C TYR* 4.1 10.1 - - + +
130C ALA* 1.3 78.5 - - - +
132C ASP* 1.3 59.4 + - - +
133C GLU* 3.3 24.0 + - + +
137C LEU* 3.1 32.1 + - - +
138C MET 3.8 0.9 - - - -
139C PRO* 3.5 42.8 - - - -
290C VAL* 4.4 7.6 - - - +
296C SER 3.5 8.7 - - - -
297C ARG* 3.9 20.4 - - + -
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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