Contacts of the helix formed by residues 394 - 401 (chain A) in PDB entry 5IWS
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 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A GLN* 5.4 0.4 + - - -
311A VAL* 5.2 5.9 - - - +
314A SER* 4.8 5.8 + - - -
315A THR* 5.5 2.9 - - - -
349A PHE 4.1 1.1 - - - -
350A LEU 3.3 12.8 - - - -
351A THR 3.7 1.2 + - - -
352A GLY* 3.4 23.1 - - - -
392A ALA* 3.9 3.0 + - - +
393A PHE* 1.3 76.7 + - - +
395A PHE* 1.3 62.3 + - - -
396A ILE 3.2 2.7 - - - -
397A GLU* 3.5 0.7 + - - +
398A LEU* 2.9 26.3 + - - +
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A THR* 4.3 11.3 + - + +
349A PHE* 3.0 66.0 + + + +
350A LEU* 3.0 11.5 + - + -
394A GLY* 1.3 69.9 - - - -
396A ILE* 1.3 64.8 + - - +
398A LEU* 3.4 27.5 - - + +
399A ILE* 3.0 49.4 + - + +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.7 28.7 - - + -
31A SER* 4.6 13.2 - - - +
32A ILE* 4.6 17.7 - - + +
35A LEU* 4.9 11.4 - - + -
350A LEU* 3.2 46.6 + - + +
351A THR* 5.3 0.2 - - + -
395A PHE* 1.3 77.4 - - + +
397A GLU* 1.3 60.7 + - - +
399A ILE* 3.2 16.4 - - + +
400A THR* 2.8 30.1 + - - +
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 5.5 1.0 - - - +
31A SER* 4.2 19.6 + - - +
34A LYS* 3.8 25.3 + - - +
391A HIS* 5.3 1.2 + - - -
392A ALA* 3.3 8.9 - - + -
393A PHE* 2.7 48.4 + - - +
394A GLY 3.5 2.9 + - - +
395A PHE 3.4 0.2 - - - -
396A ILE* 1.3 76.6 - - - +
398A LEU* 1.3 64.7 + - - +
400A THR* 3.5 10.5 - - + -
401A ARG* 3.1 60.8 + - + +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 4.5 7.4 - - + -
315A THR* 4.7 3.1 - - + +
390A VAL* 3.6 30.7 - - + -
392A ALA* 3.9 12.5 - - + +
394A GLY 2.9 15.6 + - - +
395A PHE* 3.4 36.8 - - + +
396A ILE 3.2 0.4 - - - -
397A GLU* 1.3 78.4 - - - +
399A ILE* 1.3 53.3 + - + +
401A ARG* 3.4 3.4 + - + +
402A THR* 2.7 35.2 + - - +
405A MSE 5.5 1.9 - - - +
414A LEU* 4.7 11.2 - - + +
417A PHE* 3.6 32.8 - - + -
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 3.0 47.7 + - + +
396A ILE* 3.2 22.7 - - + +
398A LEU* 1.3 74.9 - - + +
400A THR* 1.3 66.2 + - - +
402A THR* 3.3 11.5 + - - +
403A PRO* 3.3 18.5 - - - +
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER 5.6 1.1 + - - +
34A LYS* 5.9 0.9 - - + -
35A LEU* 3.4 32.7 - - + +
38A MSE 3.7 39.3 - - + +
396A ILE* 2.8 23.3 + - - +
397A GLU* 3.5 15.7 - - + -
398A LEU 3.2 0.4 - - - -
399A ILE* 1.3 80.6 - - - +
401A ARG* 1.3 61.0 + - + +
403A PRO* 3.4 15.6 - - - +
404A MSE 4.9 4.0 + - - +
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 4.2 12.5 - - - +
272A ASP* 3.7 17.8 + - - -
275A TRP* 3.5 33.7 - - + -
276A LEU* 3.8 22.8 - - - +
391A HIS* 2.4 54.0 + - - -
392A ALA* 4.4 3.1 - - + -
397A GLU* 3.1 50.8 + - + +
398A LEU* 3.7 4.7 - - + +
400A THR* 1.3 79.1 - - + +
402A THR* 1.3 64.1 + - - +
403A PRO* 3.5 1.6 - - - -
404A MSE 3.3 19.1 + - - +
405A MSE 3.2 28.7 + - + +
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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