Contacts of the helix formed by residues 324 - 333 (chain C) in PDB entry 2ZXI
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 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C ILE* 4.5 1.8 - - + -
167C GLY* 3.4 26.7 - - - +
168C ASP* 4.9 7.2 - - - +
265C ASN 5.4 2.9 - - - +
323C LEU* 1.3 98.8 - - + +
325C GLU* 1.3 66.4 + - - +
326C GLU* 3.3 27.6 - - - +
327C VAL* 3.0 18.1 + - + +
328C GLN* 3.0 18.4 + - - +
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Residues in contact with GLU 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 4.1 10.1 - - + +
323C LEU 3.5 1.2 + - - -
324C PRO* 1.3 72.2 - - - +
326C GLU* 1.3 66.7 + - - +
328C GLN* 3.0 24.2 + - - +
329C TRP* 3.1 30.3 + - + +
343C LEU* 5.1 7.6 - - + +
346C PRO* 3.6 25.5 - - + +
124D GLU* 2.5 39.7 - - - +
143D LEU* 3.8 19.8 + - + +
145D VAL* 3.6 18.9 - - + +
147D TYR* 3.8 10.2 + - - -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PRO* 3.3 28.1 - - - +
325C GLU* 1.3 78.2 + - - +
327C VAL* 1.3 68.8 + - + +
329C TRP* 3.3 30.4 + - + +
330C GLU* 3.6 17.3 + - - +
-1D SER* 3.3 28.3 - - - +
0D HIS* 4.9 3.6 - - - -
3D TRP* 4.9 3.1 + - - -
143D LEU 4.5 6.1 - - - +
144D GLY 5.1 2.7 - - - +
145D VAL* 4.1 13.4 - - + +
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ILE* 4.5 11.4 - - + +
265C ASN* 3.5 48.7 - - + +
323C LEU* 4.0 22.2 - - + -
324C PRO* 3.0 32.5 + - + +
326C GLU* 1.3 82.3 - - + +
328C GLN* 1.3 66.7 + - - +
330C GLU* 3.1 9.1 + - - +
331C MET* 2.9 21.9 + - + +
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Residues in contact with GLN 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 4.2 3.8 - - - +
321C THR* 4.3 15.5 - - + -
323C LEU* 2.7 33.7 + - + +
324C PRO 3.0 14.0 + - - +
325C GLU* 3.0 16.4 + - - +
327C VAL* 1.3 76.9 - - - +
329C TRP* 1.3 63.1 + - - +
330C GLU 3.2 0.2 + - - -
331C MET* 4.0 7.9 - - + -
332C TYR* 2.9 41.3 + - + -
343C LEU* 4.1 10.6 - - + +
346C PRO* 3.7 6.3 - - - +
347C ALA* 2.7 54.3 + - - +
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Residues in contact with TRP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C GLU* 3.1 30.2 + - + +
326C GLU* 3.3 31.6 - - + +
327C VAL 3.2 0.2 - - - -
328C GLN* 1.3 76.5 - - - +
330C GLU* 1.3 63.2 + - - +
332C TYR* 4.2 3.0 - - - +
333C ARG* 3.1 62.6 + - - +
343C LEU* 3.8 28.7 - - + +
-1D SER 5.0 0.2 - - - -
0D HIS 4.6 0.7 - - - -
1D MET 3.9 7.4 - - - -
2D ALA* 3.5 26.9 - - + -
3D TRP* 4.1 19.5 - + - +
6D ASP* 3.9 10.7 + - - -
122D LYS* 5.1 1.8 - - - +
145D VAL* 3.2 44.2 - - + -
147D TYR* 3.7 19.8 + + - -
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 4.9 1.8 + - - +
261C ILE* 3.5 40.5 - - + +
265C ASN* 4.1 12.1 + - - -
326C GLU 3.6 7.1 + - - +
327C VAL* 3.1 12.3 + - - +
329C TRP* 1.3 82.1 - - - +
331C MET* 1.3 62.1 + - - +
333C ARG* 3.5 2.6 + - - +
334C SER* 3.4 15.4 + - - -
3D TRP* 3.8 25.7 - - + -
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Residues in contact with MET 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C THR* 4.1 15.5 - - + -
261C ILE* 4.1 17.2 - - + +
262C ILE* 4.4 8.1 - - + -
287C ILE* 3.8 26.7 - - + -
319C LEU* 3.3 37.5 - - + -
321C THR* 4.5 13.0 - - - -
323C LEU* 4.4 18.4 - - + -
327C VAL* 2.9 16.5 + - + +
328C GLN* 3.5 13.5 - - - +
330C GLU* 1.3 73.9 - - - +
332C TYR* 1.3 74.1 + - + +
334C SER* 2.6 25.3 + - - -
335C ILE* 2.9 12.2 - - + +
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Residues in contact with TYR 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PRO* 3.7 0.7 - - - +
204C ALA* 3.0 38.1 + - + -
206C LEU* 4.5 7.2 - - + -
316C PRO* 3.9 12.1 - - + -
319C LEU* 2.8 59.5 + - + +
321C THR* 4.0 4.0 - - + +
328C GLN* 2.9 47.3 + - + +
329C TRP* 4.2 2.7 - - - +
331C MET* 1.3 82.5 - - + +
333C ARG* 1.3 59.7 + - - +
334C SER 3.3 1.2 + - - -
335C ILE* 3.3 9.2 + - - +
338C LEU* 3.1 37.3 - - + +
341C VAL* 4.2 15.3 - - + -
343C LEU* 4.2 15.5 - - + -
347C ALA* 3.8 3.1 - - - +
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Residues in contact with ARG 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 5.0 1.5 + - - -
329C TRP* 3.1 48.8 + - - +
330C GLU 3.9 4.3 - - - +
331C MET 3.1 0.8 - - - -
332C TYR* 1.3 73.8 - - - +
334C SER* 1.3 58.4 + - - +
335C ILE 3.3 1.6 - - - -
338C LEU 3.3 14.1 - - - +
339C GLU* 3.3 44.2 + - - +
340C ASN* 4.6 0.4 - - - +
341C VAL* 2.9 32.3 + - + +
342C VAL* 4.3 4.0 - - - +
343C LEU* 4.9 1.6 - - - +
3D TRP* 3.3 51.5 - - + +
5D VAL* 3.2 19.3 - - - +
6D ASP* 3.0 25.1 + - - -
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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