Contacts of the strand formed by residues 297 - 304 (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 ARG 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C TYR* 3.4 27.0 + - + +
130C ALA 3.5 8.3 - - - +
131C CYS* 3.9 13.7 - - + -
132C ASP* 5.1 3.4 - - - +
133C GLU* 6.1 0.9 - - - -
179C GLY 6.2 0.2 - - - -
258C ALA 5.6 1.8 + - - -
290C VAL* 4.3 0.7 - - - -
295C ALA* 3.3 5.1 - - - +
296C SER* 1.3 90.4 - - - +
298C ALA* 1.3 59.6 + - - +
299C LEU 4.2 0.2 - - - -
317C ASN 3.8 0.9 - - - +
318C THR* 3.2 33.0 + - - +
319C PHE* 3.6 28.4 - - + +
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Residues in contact with ALA 298 (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* 3.3 8.7 - - - -
130C ALA 3.0 32.2 + - - +
286C ALA* 3.7 20.6 - - - +
289C ILE* 3.8 21.8 - - + -
290C VAL* 3.7 20.1 - - + +
295C ALA* 5.1 1.6 - - + -
297C ARG* 1.3 71.7 - - - +
299C LEU* 1.3 59.7 + - - +
300C ILE* 5.6 2.0 - - + -
316C VAL* 5.8 3.8 - - + -
317C ASN 4.0 3.4 - - - -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C PHE* 3.8 26.7 - - + -
128C GLY 3.3 11.2 - - - +
129C TYR* 3.9 23.6 - - + -
259C ALA* 4.4 3.4 - - + -
260C PRO* 4.3 24.5 - - + -
297C ARG 4.2 0.2 + - - -
298C ALA* 1.3 74.1 - - - +
300C ILE* 1.3 71.8 + - - +
315C MET* 6.1 6.3 - - + -
316C VAL* 3.1 7.8 - - - +
317C ASN* 3.0 55.6 + - + +
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Residues in contact with ILE 300 (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 3.9 0.5 - - - +
127C PHE* 3.1 12.3 - - - -
128C GLY* 2.7 46.8 + - - +
282C GLY* 4.6 5.2 - - - +
285C VAL* 3.0 39.3 - - + -
286C ALA* 4.4 9.4 - - + +
289C ILE* 5.3 6.5 - - + -
298C ALA* 5.1 1.6 - - + -
299C LEU* 1.3 81.6 - - - +
301C GLN* 1.3 75.0 + - - +
302C VAL* 4.3 12.3 - - + -
314C VAL* 4.6 4.3 - - + -
315C MET 3.4 6.7 - - - +
316C VAL* 4.0 25.6 - - + -
333C VAL* 4.7 11.7 - - + -
339C LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 301 (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* 3.3 18.1 - - - +
126C MET 3.8 6.1 - - - +
127C PHE* 3.3 28.8 - - + -
300C ILE* 1.3 76.5 - - - +
302C VAL* 1.3 81.4 + - - +
313C SER* 4.9 4.3 - - - -
314C VAL* 3.3 0.8 - - - -
315C MET* 2.5 49.8 + - + +
6D LEU 4.3 4.2 - - - +
7D PHE* 3.2 33.0 - - - -
8D THR* 3.2 39.1 + - - -
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Residues in contact with VAL 302 (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* 3.4 3.6 - - - -
126C MET* 3.1 55.0 + - + +
278C ALA* 4.2 19.3 - - + +
282C GLY* 6.1 4.0 - - - -
300C ILE* 4.3 9.2 - - + -
301C GLN* 1.3 86.7 - - - +
303C SER* 1.3 62.1 + - - +
304C TYR* 4.2 9.9 - - + +
311C PRO* 4.8 2.7 - - + -
313C SER 3.1 7.6 - - - +
314C VAL* 3.9 19.1 - - + -
339C LEU* 4.0 22.2 - - + -
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Residues in contact with SER 303 (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 3.3 10.2 + - - -
125C LEU* 4.7 1.1 - - - -
301C GLN* 5.2 0.7 - - - -
302C VAL* 1.3 78.0 - - - +
304C TYR* 1.3 62.6 + - - +
311C PRO* 3.0 12.1 - - - +
312C THR* 2.8 44.6 + - - +
313C SER* 2.8 25.6 + - - -
8D THR* 3.0 26.8 - - - +
171D GLN* 3.1 3.6 + - - -
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Residues in contact with TYR 304 (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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120C ALA* 3.8 25.6 - - + -
122C ASP 4.1 5.6 - - - +
123C GLN* 3.2 9.2 - - - -
124C GLY 2.9 8.9 + - - +
126C MET* 3.8 18.4 - - - -
274C VAL* 4.1 16.8 - - + +
278C ALA* 3.6 32.6 - - + +
302C VAL* 4.2 10.2 - - + +
303C SER* 1.3 81.5 + - - +
305C ALA* 1.3 58.3 + - - +
308C VAL 4.5 1.8 - - - -
309C ALA 3.7 24.0 - - - -
311C PRO* 3.8 22.6 - - + +
312C THR* 3.6 9.4 - - - +
339C LEU* 2.7 27.4 + - - +
341C PRO* 4.1 8.5 - - + -
344C ILE* 4.9 2.4 - - - +
171D GLN* 2.9 22.5 + - - +
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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