Contacts of the helix formed by residues 333 - 341 (chain E) in PDB entry 3SWD
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 MET 333 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E THR* 3.5 46.0 - - + +
117E ILE* 5.6 2.9 - - + -
330E ASN 5.4 4.0 - - - +
331E ARG 3.9 1.2 - - - -
332E PHE* 1.3 75.3 - - - +
334E HIS* 1.3 58.4 + - - +
336E PRO* 3.0 21.3 - - - +
337E GLU* 3.7 15.2 - - + +
368E THR* 3.9 36.3 - - + +
369E ASP* 6.3 1.3 - - + -
114H GLY* 4.3 7.5 - - - -
115H QPA 3.9 37.5 - - - +
116H THR* 4.1 12.6 - - + -
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Residues in contact with HIS 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E GLN* 3.0 30.8 + - - -
308E ALA* 3.5 32.2 - - + +
311E THR* 3.7 13.1 + - + -
331E ARG* 3.1 22.5 + - - +
332E PHE* 3.9 7.9 - + - -
333E MET* 1.3 71.6 + - - +
335E VAL* 1.3 79.6 + - + +
337E GLU* 3.2 9.5 + - - +
338E LEU* 2.8 37.7 + - + +
372E ALA* 4.1 16.4 - - + +
373E SER* 5.8 1.8 - - - +
375E SER* 4.0 14.6 - - - +
376E LEU* 4.6 9.6 - - + -
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Residues in contact with VAL 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E THR* 4.2 7.6 - - + -
315E LEU* 5.6 2.4 - - + +
332E PHE* 3.0 16.9 + - + +
334E HIS* 1.3 93.6 - - + +
336E PRO* 1.3 72.7 - - + +
338E LEU* 3.1 9.5 + - - +
339E SER* 2.9 24.6 + - - +
343E ALA* 5.5 0.2 - - - +
345E ALA* 4.1 28.3 - - + +
347E ILE* 4.0 24.0 - - + -
352E VAL* 4.0 19.1 - - + -
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Residues in contact with PRO 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E PHE 3.2 11.0 - - - +
333E MET* 3.0 22.4 - - + +
335E VAL* 1.3 86.8 - - + +
337E GLU* 1.3 59.2 + - - +
339E SER* 3.1 18.9 + - - +
340E ARG* 3.2 15.8 + - - +
347E ILE* 5.0 4.9 - - + -
91H ARG* 5.9 0.2 - - - +
111H LEU* 5.2 0.2 - - - +
112H PRO 4.6 4.1 - - - +
113H GLY* 3.6 11.1 - - - +
114H GLY* 3.5 28.3 - - - +
115H QPA 5.2 0.4 - - - +
118H GLY 5.9 0.9 - - - +
119H ALA* 5.5 4.3 - - + -
120H ARG 5.3 11.4 - - - +
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Residues in contact with GLU 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E MET* 3.7 14.4 - - + +
334E HIS* 3.2 8.0 + - - +
335E VAL 3.2 0.4 - - - -
336E PRO* 1.3 72.4 - - - +
338E LEU* 1.3 67.7 + - - +
340E ARG* 3.0 28.0 + - - +
341E MET* 3.6 2.8 + - - +
365E VAL* 3.4 21.7 - - + +
366E MET* 2.9 47.6 + - - +
376E LEU* 3.7 20.6 - - + -
84H TYR* 5.2 1.2 + - - -
113H GLY* 3.6 5.9 - - - -
114H GLY* 2.9 27.6 + - - +
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Residues in contact with LEU 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E ALA 5.1 0.2 - - - +
312E LEU* 4.2 26.9 - - + +
315E LEU* 3.6 23.6 - - + -
334E HIS* 2.8 34.8 + - + +
335E VAL* 3.1 5.1 + - - +
337E GLU* 1.3 75.7 - - - +
339E SER* 1.3 57.1 + - - +
341E MET* 2.8 28.4 + - - +
343E ALA* 3.2 29.3 + - + +
360E LEU* 4.9 3.0 - - + +
375E SER* 4.6 8.3 - - - +
376E LEU* 4.0 15.9 - - + -
379E ALA* 3.7 30.5 - - + -
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Residues in contact with SER 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E VAL* 2.9 22.1 + - - +
336E PRO* 3.3 15.4 - - - +
337E GLU 3.1 0.4 - - - -
338E LEU* 1.3 70.9 - - - +
340E ARG* 1.3 60.4 + - - +
341E MET 3.0 4.9 - - - -
342E GLY* 3.2 11.1 + - - -
343E ALA* 3.7 22.0 + - - +
345E ALA* 4.8 9.0 + - - +
111H LEU* 3.7 16.0 - - - +
138H LEU* 3.6 13.5 - - - +
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Residues in contact with ARG 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E PRO 3.2 13.9 + - - +
337E GLU* 3.0 20.6 + - - +
339E SER* 1.3 76.9 - - - +
341E MET* 1.3 58.9 + - - +
342E GLY 3.3 1.2 + - - -
361E SER* 4.6 1.0 - - - +
363E ALA* 3.7 17.0 - - + +
364E GLN* 2.4 50.1 + - - +
365E VAL* 4.5 3.6 - - + -
84H TYR* 3.4 21.6 - - - +
110H SER* 3.0 25.7 + - - -
111H LEU* 2.8 33.9 + - + +
113H GLY* 4.1 16.8 - - - +
138H LEU* 4.2 6.3 - - - +
140H GLU 4.5 2.4 + - - -
141H GLY* 3.3 39.5 + - - -
142H TYR* 5.5 1.4 - - - -
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Residues in contact with MET 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E GLU 4.0 2.5 - - - +
338E LEU* 2.8 20.1 + - - +
340E ARG* 1.3 81.7 - - - +
342E GLY* 1.3 55.3 + - - +
343E ALA 3.5 0.4 - - - -
360E LEU* 3.4 15.6 - - + +
361E SER* 2.7 49.1 + - - +
363E ALA* 4.2 7.2 - - + +
365E VAL* 4.0 30.1 - - + -
376E LEU* 4.8 1.8 - - - +
379E ALA* 3.6 34.3 - - + -
380E GLY 3.8 1.3 - - - +
383E ALA* 3.5 30.3 - - + -
387E THR* 3.5 22.9 - - + +
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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