Contacts of the helix formed by residues 314 - 325 (chain A) in PDB entry 2HRC
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 GLN 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A TRP 3.1 8.7 - - - +
302A GLN* 6.0 0.7 - - - -
304A LYS* 2.5 51.1 + - + +
310A TRP* 6.5 0.2 - - + -
311A LEU 5.5 1.3 - - - +
312A GLY* 4.8 6.7 - - - -
313A PRO* 1.3 73.6 - - - +
315A THR* 1.3 63.9 + - - +
316A ASP* 3.3 24.6 + - - +
317A GLU* 2.9 37.2 + - - +
318A SER* 2.8 26.8 + - - -
771B ASN 4.9 0.2 + - - -
905B LEU* 5.8 0.4 - - - +
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Residues in contact with THR 315 (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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259A LEU* 5.1 0.4 - - + -
261A SER* 2.7 31.8 + - - +
300A VAL* 3.4 22.5 - - + +
301A TRP 2.8 25.3 + - - -
302A GLN* 3.4 5.0 + - - +
313A PRO 3.7 0.2 + - - -
314A GLN* 1.3 71.8 - - - +
316A ASP* 1.3 62.9 + - - +
318A SER* 3.3 2.6 + - - -
319A ILE* 3.0 39.6 + - + +
332A LEU* 4.6 7.2 - - + -
348A LEU* 4.2 5.4 - - + -
352A TYR* 3.7 22.9 + - + -
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Residues in contact with ASP 316 (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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314A GLN* 3.3 28.8 + - - +
315A THR* 1.3 76.3 - - - +
317A GLU* 1.3 80.3 + - - +
319A ILE* 3.3 6.4 + - - +
320A LYS* 3.1 23.2 + - - +
351A GLU* 5.2 1.7 - - - +
352A TYR* 3.7 43.0 + - + -
355A VAL* 5.5 9.5 - - + +
356A LEU* 4.3 9.7 - - + +
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Residues in contact with GLU 317 (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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314A GLN* 2.9 45.5 + - - +
315A THR 3.4 0.4 - - - -
316A ASP* 1.3 94.9 + - - +
318A SER* 1.3 56.6 + - - +
320A LYS* 3.8 8.2 - - - +
321A GLY 2.8 22.7 + - - -
771B ASN 5.7 0.3 - - - +
905B LEU* 3.6 30.3 - - + +
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Residues in contact with SER 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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259A LEU* 4.3 6.5 - - - -
300A VAL* 3.5 18.5 - - - +
313A PRO* 3.4 22.3 - - - +
314A GLN 2.8 21.7 + - - -
315A THR 3.6 4.7 - - - -
316A ASP 3.2 0.2 - - - -
317A GLU* 1.3 75.8 - - - +
319A ILE* 1.3 60.4 + - - +
322A LEU* 2.9 36.6 + - - +
904B PRO* 3.6 22.7 - - - +
905B LEU* 4.9 3.0 - - - +
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Residues in contact with ILE 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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259A LEU* 3.9 18.2 - - + -
315A THR* 3.0 19.8 + - + +
316A ASP* 3.3 6.3 + - - +
318A SER* 1.3 75.7 - - - +
320A LYS* 1.3 63.6 + - - +
322A LEU* 3.4 2.3 + - - +
323A CYS* 3.1 22.4 + - + +
330A ILE* 3.9 16.2 - - + +
332A LEU* 3.9 22.4 - - + -
352A TYR* 3.8 27.8 - - + -
356A LEU* 3.3 27.6 - - + -
362A VAL* 4.9 5.8 - - + -
365A ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 320 (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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316A ASP 3.1 17.0 + - - +
317A GLU* 3.8 7.6 - - - +
319A ILE* 1.3 78.2 - - - +
321A GLY* 1.3 61.3 + - - +
323A CYS* 3.4 6.1 + - - +
324A GLU* 2.9 69.4 + - + +
356A LEU* 4.0 19.7 - - + +
360A CYS* 5.3 7.0 - - + -
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Residues in contact with GLY 321 (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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317A GLU 2.8 18.0 + - - -
318A SER 3.3 0.9 + - - -
320A LYS* 1.3 77.8 - - - +
322A LEU* 1.3 59.9 + - - +
324A GLU* 3.4 3.9 + - - -
325A ARG* 2.9 41.8 + - - +
904B PRO 3.2 20.2 - - - -
905B LEU* 3.9 6.3 - - - +
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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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257A VAL* 4.2 11.7 - - + -
259A LEU* 3.7 37.7 - - + -
318A SER 2.9 21.7 + - - +
319A ILE 3.6 3.8 - - - +
321A GLY* 1.3 77.0 - - - +
323A CYS* 1.3 63.7 + - - +
325A ARG* 3.0 12.9 + - + +
326A GLY 3.2 0.2 + - - -
327A ARG* 2.9 44.3 + - + +
330A ILE* 3.9 14.4 - - + -
901B LEU* 3.9 28.0 - - + -
902B SER 4.8 0.9 - - - +
904B PRO* 3.7 22.6 + - + -
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Residues in contact with CYS 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 ILE* 3.1 16.8 + - + +
320A LYS* 3.7 6.3 - - - +
322A LEU* 1.3 75.7 - - - +
324A GLU* 1.3 62.3 + - - +
325A ARG 3.2 0.7 + - - -
326A GLY 3.2 8.1 + - - -
327A ARG 3.5 10.2 + - - +
328A LYS* 2.8 54.9 + - + -
330A ILE* 4.9 1.5 - - + +
360A CYS* 3.3 37.2 - - + +
361A GLY 3.6 11.0 - - - -
362A VAL* 4.0 13.2 - - + -
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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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320A LYS* 2.9 57.1 + - + +
321A GLY* 3.8 5.8 - - - +
323A CYS* 1.3 76.1 - - - +
325A ARG* 1.3 72.6 + - - +
326A GLY 3.4 1.5 + - - -
328A LYS* 5.0 0.2 - - - +
360A CYS* 3.1 34.2 - - - -
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Residues in contact with ARG 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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321A GLY* 2.9 30.2 + - - +
322A LEU* 3.0 7.8 + - + +
324A GLU* 1.3 93.9 + - - +
326A GLY* 1.3 56.6 + - - +
327A ARG* 3.5 12.7 + - + +
902B SER* 6.2 1.8 - - - -
903B CYS 4.0 9.9 - - - -
904B PRO* 3.2 25.2 + - - -
905B LEU* 3.4 19.4 + - - +
906B CYS* 2.8 34.2 + - - +
907B VAL* 3.9 10.3 - - - +
912B ARG* 4.6 14.4 + - - +
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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