Contacts of the helix formed by residues 345 - 355 (chain E) in PDB entry 4K4I
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 345 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339E SER* 4.2 9.2 - - - -
344E ALA* 1.3 73.5 - - - +
346E THR* 1.3 65.7 + - - -
347E LYS 3.2 2.7 - - - -
348E THR* 4.0 0.2 - - - -
349E ALA* 2.9 24.3 + - - +
4G T 2.8 28.0 + - - -
5G A 4.0 10.5 - - - -
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Residues in contact with THR 346 (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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268E SER* 3.3 27.4 - - - +
269E VAL* 3.3 25.0 - - - +
271E GLY* 4.0 16.5 - - - +
335E LEU* 5.4 0.2 - - - +
339E SER* 5.1 3.8 - - - -
345E GLY* 1.3 72.3 - - - -
347E LYS* 1.3 67.5 + - - +
349E ALA* 3.9 4.1 - - - +
350E GLN* 2.9 37.6 + - - +
4G T 3.5 4.9 + - - -
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Residues in contact with LYS 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLY* 6.2 1.8 - - - -
346E THR* 1.3 82.0 + - - +
348E THR* 1.3 67.4 + - - +
350E GLN* 3.1 14.4 + - - +
351E MET* 2.8 26.2 + - - +
3G G 3.7 49.8 - - + +
4G T 3.0 20.8 + - - +
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Residues in contact with THR 348 (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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344E ALA* 4.1 2.2 - - + -
345E GLY 4.0 7.2 - - - -
347E LYS* 1.3 75.0 - - - +
349E ALA* 1.3 58.8 + - - +
351E MET* 3.3 13.3 + - + +
352E TRP* 2.9 74.7 + - + +
373E GLN* 3.9 18.4 + - - +
3G G 4.0 3.3 + - - -
4G T 2.6 25.3 + - - -
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Residues in contact with ALA 349 (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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269E VAL 5.6 0.9 - - - +
335E LEU* 3.6 25.8 - - + +
338E PHE* 3.7 34.1 - - + -
339E SER* 4.2 4.7 - - - +
344E ALA* 5.3 0.6 - - + +
345E GLY 2.9 19.8 + - - +
346E THR* 3.9 5.4 - - - +
347E LYS 3.2 0.2 - - - -
348E THR* 1.3 78.4 - - - +
350E GLN* 1.3 56.7 + - - +
352E TRP* 3.3 4.5 + - - +
353E TYR* 2.9 28.8 + - - +
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Residues in contact with GLN 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E VAL 4.3 2.9 + - - -
270E GLN* 3.1 39.2 + - - +
271E GLY* 4.9 2.4 - - - -
335E LEU* 3.9 18.8 - - + +
346E THR* 2.9 29.1 + - - +
347E LYS* 3.6 15.4 + - - +
349E ALA* 1.3 73.3 - - - +
351E MET* 1.3 67.5 + - - +
353E TYR* 2.8 5.6 + - + +
354E GLN* 2.8 39.5 + - - +
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Residues in contact with MET 351 (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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347E LYS 2.8 19.4 + - - +
348E THR* 3.5 11.4 - - + +
350E GLN* 1.3 71.3 - - - +
352E TRP* 1.3 102.3 + - + +
354E GLN* 3.1 14.2 + - - +
355E GLN* 3.0 38.1 + - + +
368E SER 5.9 1.1 - - - +
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Residues in contact with TRP 352 (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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338E PHE* 3.7 29.4 - + + -
341E ILE* 3.9 24.2 - - + -
344E ALA* 4.0 15.9 - - + -
348E THR* 2.9 42.0 + - + +
349E ALA* 3.7 1.8 - - - +
351E MET* 1.3 105.2 - - + +
353E TYR* 1.3 62.7 + - - +
355E GLN* 3.3 11.4 + - - -
357E PHE* 2.9 49.9 + + + +
363E ILE* 3.6 18.2 - - + -
367E ALA* 3.7 14.0 - - + +
368E SER 4.3 8.7 + - - +
369E LEU* 3.7 31.4 - - + -
373E GLN* 4.4 8.1 - - + -
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Residues in contact with TYR 353 (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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330E GLU* 4.6 2.6 - - - +
331E SER* 3.4 44.1 + - - -
334E VAL* 3.6 27.1 - - + -
335E LEU* 3.9 13.9 - - + -
338E PHE* 4.2 2.0 - - + -
349E ALA 2.9 13.1 + - - +
350E GLN* 2.8 11.3 + - + +
352E TRP* 1.3 76.9 - - - +
354E GLN* 1.3 65.9 + - + +
356E GLY* 2.9 15.9 + - - -
357E PHE 3.9 5.8 - - - -
358E ARG* 3.1 56.5 + - - -
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Residues in contact with GLN 354 (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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350E GLN* 2.8 29.8 + - + +
351E MET* 3.1 14.3 + - - +
353E TYR* 1.3 82.5 - - + +
355E GLN* 1.3 58.6 + - + +
356E GLY* 3.0 5.9 + - - -
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Residues in contact with GLN 355 (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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351E MET* 3.0 44.5 + - + +
352E TRP* 3.3 8.2 + - - +
354E GLN* 1.3 75.9 - - - +
356E GLY* 1.3 58.4 - - - +
357E PHE* 3.2 41.5 + - + -
366E GLN 5.2 2.2 + - - -
367E ALA* 5.8 0.4 - - - +
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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