Contacts of the helix formed by residues 351 - 363 (chain A) in PDB entry 1YV5
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 PRO 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU* 4.0 21.8 - - + +
85A LEU* 3.7 19.3 - - + -
349A PRO 3.9 2.2 - - - +
350A LEU* 1.4 86.9 - - + +
352A PRO* 1.3 73.5 - - + +
353A ALA* 3.0 11.7 + - + +
354A VAL* 3.0 27.4 + - + +
355A PHE* 4.1 4.4 - - - -
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Residues in contact with PRO 352 (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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343A ILE* 4.2 14.6 - - + +
347A ALA* 4.3 17.3 - - + -
348A ALA 5.9 0.2 - - - +
350A LEU 3.2 7.8 - - - +
351A PRO* 1.3 82.6 - - + +
353A ALA* 1.3 62.6 + - - +
355A PHE* 2.9 9.4 + - + +
356A LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 353 (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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84A GLU* 3.8 19.0 - - - +
351A PRO* 3.0 8.4 + - + -
352A PRO* 1.3 79.6 - - - +
354A VAL* 1.3 61.5 + - - +
356A LEU* 4.2 13.6 - - + +
357A GLY* 3.0 20.3 + - - -
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Residues in contact with VAL 354 (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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80A VAL* 6.1 1.4 - - - +
81A ALA* 4.5 9.2 - - + -
84A GLU* 2.9 35.0 - - + +
85A LEU* 4.2 23.1 - - + -
224A ILE* 3.6 35.3 - - + +
350A LEU* 5.7 2.0 - - + -
351A PRO* 3.0 17.9 + - + +
352A PRO 2.9 0.6 + - - -
353A ALA* 1.3 81.0 - - - +
355A PHE* 1.3 77.7 + - + +
357A GLY* 3.7 0.7 + - - -
358A LEU* 3.6 19.9 + - - +
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Residues in contact with PHE 355 (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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224A ILE* 4.7 2.2 - - + -
242A ALA* 4.1 11.9 - - + -
245A ILE* 3.7 31.6 - - + -
246A LEU* 3.9 36.6 - - + -
249A MET* 3.4 9.2 - - + +
343A ILE* 3.5 24.7 - - + -
347A ALA* 3.8 36.6 - - + -
350A LEU* 3.8 34.8 - - + -
351A PRO 4.1 7.6 - - - -
352A PRO 2.9 5.0 + - - +
354A VAL* 1.3 85.6 - - + +
356A LEU* 1.3 59.4 + - - +
358A LEU* 3.3 8.3 + - + +
359A ALA* 2.9 23.7 + - - +
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Residues in contact with LEU 356 (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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340A MET* 3.5 31.8 - - + +
343A ILE* 4.3 11.7 - - + -
352A PRO* 2.9 36.1 + - + +
353A ALA* 4.0 9.4 - - + +
355A PHE* 1.3 74.4 - - - +
357A GLY* 1.3 60.9 + - - +
359A ALA* 3.7 4.6 - - - +
360A ARG* 3.1 27.5 + - - +
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Residues in contact with GLY 357 (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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80A VAL* 6.5 1.1 - - - -
353A ALA 3.0 16.1 + - - -
354A VAL 4.3 0.9 - - - -
356A LEU* 1.3 74.6 - - - +
358A LEU* 1.3 64.7 + - - +
360A ARG* 3.6 8.4 - - - +
361A LYS* 3.3 24.1 + - - +
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Residues in contact with LEU 358 (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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77A THR* 4.2 23.1 - - + +
219A SER 5.8 0.4 - - - +
220A PHE* 3.6 33.9 - - + +
224A ILE* 3.8 24.5 - - + -
246A LEU* 3.7 30.3 - - + -
249A MET* 4.2 8.1 - - - -
354A VAL 3.6 11.8 + - - +
355A PHE* 3.3 11.6 + - + +
357A GLY* 1.3 75.2 - - - +
359A ALA* 1.3 66.3 + - - +
361A LYS* 3.1 16.0 + - + +
362A ILE* 3.1 21.0 + - + +
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Residues in contact with ALA 359 (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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249A MET* 3.9 12.5 - - + +
336A TYR* 4.6 3.6 - - + -
339A ILE* 5.1 0.2 - - + -
340A MET* 3.2 35.0 - - + -
355A PHE 2.9 15.7 + - - +
356A LEU 3.7 4.3 - - - +
358A LEU* 1.3 76.5 - - - +
360A ARG* 1.3 63.3 + - - +
361A LYS 3.2 0.3 + - - -
362A ILE* 3.2 3.4 + - - -
363A TYR* 3.0 43.2 + - + +
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Residues in contact with ARG 360 (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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336A TYR* 5.4 2.2 - - - -
356A LEU 3.1 17.4 + - - +
357A GLY* 3.6 9.2 - - - +
359A ALA* 1.3 77.2 - - - +
361A LYS* 1.3 66.5 + - + +
363A TYR* 3.9 1.2 - - - -
364A LYS* 3.3 30.1 + - + +
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Residues in contact with LYS 361 (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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27A GLU* 5.9 3.1 + - - -
71A LYS* 5.5 3.6 + - - -
73A ASN* 3.7 43.8 + - + +
76A LEU* 6.4 2.0 - - - -
357A GLY 3.3 9.8 + - - +
358A LEU* 3.1 14.8 + - + +
360A ARG* 1.3 84.6 - - + +
362A ILE* 1.3 62.4 + - + +
364A LYS* 3.5 20.7 - - + +
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Residues in contact with ILE 362 (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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73A ASN* 5.6 4.3 - - + +
220A PHE* 3.7 30.1 - - + -
249A MET* 3.7 41.1 - - + +
252A PHE* 3.9 10.3 - - + -
253A PHE* 4.2 18.6 - - + -
256A GLN* 3.2 28.8 + - - +
358A LEU* 3.1 17.7 + - + +
359A ALA* 3.8 3.1 - - - +
361A LYS* 1.3 78.4 - - + +
363A TYR* 1.3 86.8 + - + +
364A LYS 3.2 6.9 + - - -
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Residues in contact with TYR 363 (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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249A MET* 4.7 2.6 - - + -
252A PHE* 3.4 43.6 - + + +
256A GLN* 5.4 0.7 - - - -
332A GLU* 3.7 41.5 - - + +
335A SER* 3.0 17.9 + - - -
336A TYR* 3.7 42.6 - + + -
339A ILE* 3.1 25.4 - - + +
359A ALA* 3.0 30.0 + - + +
360A ARG* 3.9 2.9 - - - -
362A ILE* 1.3 90.2 - - + +
364A LYS* 1.3 62.7 + - - +
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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