Contacts of the helix formed by residues 317 - 328 (chain A) in PDB entry 4XH9
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 LYS 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A SER* 3.0 35.8 + - - +
314A ARG* 2.9 17.7 + - - +
316A VAL* 1.3 85.9 - - - +
318A TYR* 1.3 63.9 + - - +
319A PRO 3.4 0.2 - - - -
320A LEU* 3.0 11.7 + - + +
321A LEU* 2.9 31.8 + - + +
38B VAL* 4.0 31.9 - - + -
39B PHE 4.1 19.2 + - - +
40B GLU* 3.7 14.9 + - - +
59B ASP* 5.1 8.9 + - - +
61B ALA* 3.6 31.4 - - - +
63B GLN* 5.9 1.6 - - - +
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Residues in contact with TYR 318 (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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182A MET* 4.8 13.2 - - + -
186A GLU* 2.4 37.6 + - - -
229A HIS* 3.5 11.7 - + - -
256A TRP* 3.3 27.9 - + - -
257A LEU* 4.5 7.2 - - + -
260A LEU* 3.6 28.7 - - + -
314A ARG* 3.4 36.9 + - + +
315A LEU* 3.5 23.8 + - + +
317A LYS* 1.3 77.2 - - - +
319A PRO* 1.4 64.3 - - + +
321A LEU* 3.3 12.6 + - + +
322A LEU* 2.9 38.7 + - + +
346A ILE* 3.9 12.6 - - + -
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Residues in contact with PRO 319 (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 LEU 3.6 8.5 - - - +
316A VAL 3.6 15.7 - - - +
318A TYR* 1.4 92.7 - - + +
320A LEU* 1.3 59.3 + - + +
322A LEU* 3.8 3.6 - - + +
323A LYS* 3.0 53.9 + - - +
343A ILE* 5.5 2.0 - - + -
346A ILE* 3.9 21.3 - - + -
347A GLN* 5.0 8.5 - - + +
350A LEU* 3.6 20.9 - - + -
66B TYR* 5.0 6.3 - - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL 4.1 6.7 - - - +
317A LYS* 3.0 23.1 + - + +
319A PRO* 1.3 78.6 - - + +
321A LEU* 1.3 65.4 + - - +
323A LYS* 4.0 13.9 - - + +
324A GLU* 3.1 23.4 + - - +
37B THR* 3.9 15.6 - - + +
38B VAL* 4.2 13.0 - - + -
61B ALA* 4.1 17.0 - - + -
62B GLY* 4.0 28.9 - - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA* 5.0 3.4 - - - +
181A GLU* 4.1 22.7 - - + +
182A MET* 4.1 30.7 - - + +
314A ARG* 3.7 38.4 - - - +
317A LYS* 2.9 23.3 + - + +
318A TYR* 3.3 11.2 + - + +
320A LEU* 1.3 76.8 - - - +
322A LEU* 1.3 63.0 + - - +
324A GLU* 3.3 6.6 + - + +
325A ILE* 3.1 28.7 + - + +
37B THR* 4.8 3.8 - - - -
38B VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 322 (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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182A MET* 4.0 18.8 - - + -
253A LEU* 3.7 32.3 - - + -
257A LEU* 3.6 29.4 - - + -
318A TYR* 2.9 22.2 + - + +
319A PRO 3.8 3.4 - - - +
321A LEU* 1.3 77.9 - - + +
323A LYS* 1.3 57.2 + - - +
325A ILE* 3.2 9.7 + - + +
326A LEU* 3.0 27.2 + - - +
339A LEU* 4.5 11.0 - - + +
342A ALA* 3.7 21.8 - - + +
343A ILE* 4.0 14.3 - - + +
346A ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 323 (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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319A PRO* 3.0 31.5 + - - +
320A LEU* 4.1 14.3 - - + +
321A LEU 3.4 0.2 - - - -
322A LEU* 1.3 77.5 - - - +
324A GLU* 1.3 57.2 + - - +
326A LEU* 3.7 8.5 - - + +
327A LYS* 2.9 28.4 + - - +
343A ILE* 3.6 26.5 - - + -
347A GLN* 3.7 26.6 - - - +
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Residues in contact with GLU 324 (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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178A ALA* 3.9 17.3 - - + -
181A GLU* 5.4 0.2 - - - +
320A LEU 3.1 18.6 + - - +
321A LEU* 3.6 6.7 - - + +
322A LEU 3.2 0.2 - - - -
323A LYS* 1.3 75.2 - - - +
325A ILE* 1.3 65.0 + - - +
327A LYS* 3.3 23.7 + - - +
328A HIS* 2.8 52.4 + - - +
34B TYR* 4.6 7.9 + - - +
37B THR* 3.3 31.8 + - + +
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Residues in contact with ILE 325 (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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175A ARG* 3.8 12.5 - - + +
178A ALA* 3.7 25.8 - - + +
179A ILE* 3.9 31.4 - - + +
182A MET* 3.9 31.9 - - + -
249A ILE* 4.5 12.1 - - + -
253A LEU* 4.9 3.8 - - + -
321A LEU 3.1 17.4 + - - +
322A LEU* 3.5 10.3 - - - +
324A GLU* 1.3 76.8 - - - +
326A LEU* 1.3 55.5 + - - +
328A HIS 3.2 9.9 + - - -
329A THR* 2.6 26.4 + - - +
339A LEU* 3.7 17.9 - - + -
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Residues in contact with LEU 326 (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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171A ARG* 4.8 0.3 + - - -
322A LEU 3.0 16.3 + - - +
323A LYS* 3.7 7.0 - - + +
324A GLU 3.3 0.2 - - - -
325A ILE* 1.3 75.6 - - - +
327A LYS* 1.3 64.0 + - - +
329A THR* 3.1 17.1 + - - +
336A VAL* 3.8 44.4 - - + +
339A LEU* 3.6 20.4 - - + +
340A GLU* 3.9 23.3 - - + +
343A ILE* 3.9 20.2 - - + -
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Residues in contact with LYS 327 (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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171A ARG* 3.2 20.1 + - - -
323A LYS 2.9 15.0 + - - +
324A GLU* 3.4 31.6 + - - +
325A ILE 3.2 0.4 - - - -
326A LEU* 1.3 77.2 - - - +
328A HIS* 1.3 77.6 + - + +
329A THR 3.4 0.2 - - - -
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 3.3 41.7 + - + +
172A GLU* 4.6 1.2 - - - +
174A ARG* 3.5 50.8 + - + +
175A ARG* 3.4 24.9 - - + +
178A ALA* 4.7 0.2 - - + -
324A GLU* 2.8 50.5 + - + -
325A ILE 3.2 5.5 + - - +
326A LEU 3.2 0.6 - - - -
327A LYS* 1.3 98.6 + - + +
329A THR* 1.3 58.7 + - - +
330A PRO* 3.6 6.4 - - - +
34B TYR* 5.5 1.2 + - - -
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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