Contacts of the helix formed by residues 306 - 318 (chain B) in PDB entry 2MUC
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 SER 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B GLU* 4.3 0.2 + - - -
305B GLY* 1.3 71.5 - - - -
307B ILE* 1.3 57.7 + - - +
309B THR* 4.2 1.8 - - - -
310B LEU* 2.8 36.8 + - - +
331B PRO* 3.6 6.6 - - - +
337B GLU* 2.5 33.3 + - - -
339B VAL* 3.9 22.8 - - - +
343B PRO* 3.1 27.1 - - - +
360B LEU* 3.9 11.4 - - - -
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.3 14.1 - - + -
48B ILE* 3.9 30.5 - - + +
49B GLY* 3.6 41.7 - - - +
50B GLU* 3.4 11.6 + - + +
305B GLY 3.3 1.0 - - - -
306B SER* 1.3 76.3 - - - +
308B GLY* 1.3 58.9 + - - +
310B LEU* 3.8 1.7 - - - +
311B ALA* 2.9 27.6 + - + +
338B ILE* 3.9 25.8 - - + -
339B VAL* 3.9 18.1 - - + +
358B LEU* 3.9 10.7 - - + +
360B LEU* 3.7 8.1 - - + -
362B LEU* 4.4 1.1 - - + -
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Residues in contact with GLY 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 2.9 27.9 + - - -
274B ILE* 3.9 7.1 - - - +
304B GLU* 3.8 19.1 - - - -
307B ILE* 1.3 73.2 - - - +
309B THR* 1.3 64.0 + - - +
311B ALA* 3.8 7.3 - - - +
312B SER* 2.8 30.4 + - - -
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Residues in contact with THR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 4.8 3.1 + - - -
304B GLU* 3.0 18.3 + - - +
305B GLY 2.7 22.7 + - - -
306B SER* 3.8 3.6 - - - -
308B GLY* 1.3 76.3 - - - +
310B LEU* 1.3 61.0 + - + +
312B SER* 3.3 7.2 + - - -
313B ALA* 2.8 27.8 + - - +
328B LEU* 3.7 33.2 - - + +
330B GLY* 4.5 1.9 + - - -
331B PRO* 3.3 22.9 - - + +
343B PRO* 6.1 0.2 - - + -
345B TYR* 4.3 1.1 - - - +
350B LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B SER* 2.8 29.6 + - - +
307B ILE 3.9 2.7 - - - +
309B THR* 1.3 84.5 - - + +
311B ALA* 1.3 60.6 + - - +
313B ALA* 4.1 2.2 - - - -
314B HIS* 2.8 59.0 + - + +
343B PRO* 4.9 15.0 - - + -
350B LEU* 5.2 2.7 - - + -
351B HIS 5.7 0.2 - - - +
352B ILE* 3.7 31.9 - - + -
353B PRO* 4.8 8.1 - - + -
358B LEU* 3.8 17.9 - - + +
360B LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B SER* 3.6 31.0 - - - +
124B VAL* 5.4 1.0 - - - +
274B ILE* 4.1 7.6 - - + -
280B PRO* 3.7 23.1 - - + +
307B ILE 2.9 17.9 + - - +
308B GLY* 3.8 7.2 - - - +
309B THR 3.3 0.2 - - - -
310B LEU* 1.3 77.7 - - - +
312B SER* 1.3 63.6 + - - +
314B HIS* 3.8 3.2 + - - +
315B ALA 3.7 9.2 + - - -
358B LEU* 4.0 18.8 - - + +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 3.5 30.1 + - - +
300B GLY 4.6 4.0 + - - -
301B THR* 5.7 0.2 - - - -
304B GLU* 4.5 6.2 + - - -
308B GLY 2.8 18.2 + - - -
309B THR* 3.4 7.6 - - - -
311B ALA* 1.3 73.8 - - - +
313B ALA* 1.3 57.0 + - - +
315B ALA* 2.8 27.4 + - - +
316B PHE* 3.0 36.8 + - - -
328B LEU* 3.9 13.0 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 3.9 21.2 - - + +
309B THR 2.8 17.7 + - - +
310B LEU* 3.8 4.5 - - - +
312B SER* 1.3 76.7 - - - +
314B HIS* 1.3 61.7 + - - +
316B PHE* 2.9 13.7 + - - +
317B LEU* 3.0 19.2 + - - +
328B LEU* 4.0 8.9 - - + +
350B LEU* 4.5 2.2 - - + -
352B ILE* 3.5 31.9 - - + -
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 4.2 7.7 - - - +
124B VAL* 3.6 23.1 + - + -
125B SER* 3.2 63.6 - - - +
128B LEU* 4.1 1.2 - - - +
310B LEU* 2.8 42.8 + - + +
311B ALA* 4.1 3.6 - - - +
312B SER 3.2 0.2 - - - -
313B ALA* 1.3 76.9 - - - +
315B ALA* 1.3 60.3 + - - +
317B LEU* 3.9 6.5 + - - -
318B THR* 3.7 6.1 - - - +
352B ILE* 3.5 27.1 - - + +
353B PRO* 4.3 5.3 + - + -
355B THR 5.0 0.8 + - - -
357B GLY 3.6 13.6 + - - -
358B LEU* 3.7 18.5 - - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 3.8 16.6 - - + +
280B PRO* 3.9 24.2 - - + +
283B VAL* 4.0 15.5 - - + -
284B LEU* 3.5 10.1 - - + +
311B ALA 3.7 8.6 + - - +
312B SER* 2.8 11.9 + - - +
314B HIS* 1.3 80.2 - - - +
316B PHE* 1.3 64.1 + - + +
317B LEU 3.2 0.2 - - - -
318B THR* 2.8 26.4 + - - -
319B LEU* 4.0 1.2 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 3.1 17.2 + - - -
136B LEU* 4.0 9.4 - - + -
272B LEU* 3.5 44.0 - - + -
273B LYS* 5.3 0.2 - - - -
274B ILE* 5.2 2.2 - - + -
283B VAL* 4.4 15.9 - - + -
284B LEU* 5.8 0.4 - - + -
299B GLY* 3.4 28.3 - - - -
300B GLY 4.1 5.4 - - - -
312B SER* 3.6 31.4 - - - -
313B ALA 2.9 7.0 + - - +
315B ALA* 1.3 82.3 - - + +
317B LEU* 1.3 60.8 + - - +
319B LEU* 3.3 28.3 + - + +
322B LEU* 3.8 18.0 - - + +
326B THR* 4.3 3.1 - - + -
328B LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER* 4.1 9.4 - - - -
131B ARG* 3.7 45.5 - - + +
132B VAL* 2.8 35.3 + - - +
133B ARG* 3.5 34.7 + - + +
134B ASP 4.1 10.5 - - - -
136B LEU* 4.0 20.2 - - + -
313B ALA 3.0 18.4 + - - +
314B HIS* 4.0 7.0 - - - +
315B ALA 3.2 0.4 - - - -
316B PHE* 1.3 77.4 - - - +
318B THR* 1.3 57.3 + - - +
319B LEU 3.2 0.2 - - - -
352B ILE* 3.9 24.5 - - + -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B SER* 3.5 26.0 - - - +
128B LEU* 4.0 20.6 - - + +
129B GLY* 5.7 0.4 - - - -
130B GLY 3.6 21.0 - - - +
132B VAL* 4.3 9.1 - - - +
284B LEU* 3.5 18.5 - - - +
314B HIS 3.7 15.0 - - - +
315B ALA 2.8 15.7 + - - +
316B PHE 3.2 0.2 - - - -
317B LEU* 1.3 77.1 - - - +
319B LEU* 1.3 64.3 + - - +
320B ARG* 3.6 1.6 + - - -
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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
------------------------------------------------------------
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