Contacts of the helix formed by residues 316 - 325 (chain A) in PDB entry 4TMU
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 ASN 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLN* 6.2 2.2 - - - +
314A PRO* 3.3 2.8 - - - +
315A ARG* 1.3 99.4 + - - +
317A ILE* 1.3 62.4 + - - +
318A GLU* 3.3 15.4 + - - +
319A SER* 2.7 42.2 + - - -
320A TYR 3.2 15.4 + - - -
364A GLU* 6.0 4.0 - - - +
367A LYS* 3.8 36.2 - - + +
371A MET* 3.7 14.8 - - - +
388A TYR* 5.7 0.4 - - - +
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Residues in contact with ILE 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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316A ASN* 1.3 73.0 - - - +
318A GLU* 1.3 60.7 + - - +
320A TYR* 3.3 3.3 + - + +
321A TYR* 2.8 26.9 + - - +
367A LYS 4.3 2.4 + - - +
370A ALA* 3.6 25.6 - - + +
371A MET* 3.8 27.6 - - + +
374A PHE* 4.3 13.0 - - + -
384A VAL* 5.0 6.5 - - + -
385A LEU* 3.8 25.4 - - + -
388A TYR* 3.5 53.2 + - + -
389A PHE* 3.9 7.6 - - + -
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Residues in contact with GLU 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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149A HIS* 5.8 0.3 - - - +
153A GLN* 5.9 2.9 - - - +
183A THR* 3.5 27.8 - - + +
184A ALA* 3.6 4.0 - - - -
185A ASP* 3.0 30.6 + - - +
188A THR* 2.6 26.0 + - - +
316A ASN* 3.3 10.4 + - - +
317A ILE* 1.3 79.0 - - - +
319A SER* 1.3 57.5 + - - +
321A TYR 3.4 0.2 + - - -
322A GLN* 2.9 30.6 + - - +
367A LYS* 2.7 28.8 + - - +
388A TYR* 4.6 1.5 + - + -
389A PHE* 3.9 15.7 - - + -
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Residues in contact with SER 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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153A GLN* 5.5 5.2 + - - -
294A VAL* 5.9 4.3 - - - -
314A PRO* 4.1 13.7 - - - -
315A ARG* 4.1 10.1 - - - +
316A ASN* 2.7 36.0 + - - -
318A GLU* 1.3 69.9 - - - +
320A TYR* 1.3 62.3 + - - +
322A GLN* 3.8 9.5 - - - +
323A GLU* 2.9 46.7 + - - +
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Residues in contact with TYR 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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215A TYR* 3.3 31.9 - + - +
216A MET 4.7 6.6 + - - -
310A HIS* 3.8 24.2 - + - -
314A PRO* 3.9 17.4 - - + +
316A ASN 3.2 11.7 + - - +
317A ILE* 3.5 7.2 - - + +
318A GLU 3.3 0.2 - - - -
319A SER* 1.3 79.5 - - - +
321A TYR* 1.3 53.3 + - - +
323A GLU 3.3 0.2 + - - -
324A THR* 2.7 61.6 + - + +
336A ALA* 4.3 5.0 - - + +
337A MET 6.1 0.4 - - - -
338A LEU* 4.5 15.3 - - + +
371A MET* 3.9 20.0 - - + -
374A PHE* 3.5 36.1 - + - -
385A LEU* 4.0 19.5 - - + -
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Residues in contact with TYR 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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48A PRO* 3.6 23.6 + - + +
183A THR* 3.6 23.6 - - + -
208A PHE* 2.5 59.8 + + + -
210A ARG* 4.0 14.8 - - + +
215A TYR* 4.2 18.2 - - - -
317A ILE* 2.8 21.6 + - + +
318A GLU 3.8 2.9 - - - +
320A TYR* 1.3 75.1 - - - +
322A GLN* 1.3 58.0 + - - +
324A THR* 3.2 5.6 + - - -
325A GLY* 2.9 29.2 + - - -
385A LEU* 4.7 14.8 - - + -
386A LEU* 5.6 2.5 - - + -
389A PHE* 3.8 26.0 - + + -
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Residues in contact with GLN 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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147A GLU* 5.1 0.8 + - - -
149A HIS* 3.2 37.9 + - - -
153A GLN* 4.9 8.5 + - - +
182A ALA* 6.5 0.4 - - + -
183A THR* 3.9 20.8 + - - +
298A MET* 4.6 8.5 - - - +
318A GLU 2.9 17.4 + - - +
319A SER* 3.8 9.9 - - - +
321A TYR* 1.3 79.9 - - - +
323A GLU* 1.3 64.6 + - - +
325A GLY* 3.6 6.5 + - - -
326A ARG* 3.6 40.3 + - - +
329A ARG* 4.9 2.3 + - - -
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Residues in contact with GLU 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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242A TYR* 3.7 22.6 - - + +
294A VAL* 3.5 34.0 - - - +
308A VAL* 3.5 17.6 - - - +
310A HIS* 2.9 32.4 + - - +
314A PRO* 4.1 8.0 - - - +
319A SER* 2.9 28.8 + - - +
322A GLN* 1.3 80.4 - - - +
324A THR* 1.3 63.8 + - - +
325A GLY 3.1 2.3 + - - -
326A ARG* 3.3 37.5 + - - +
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Residues in contact with THR 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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213A ILE* 3.6 7.2 - - - +
215A TYR* 3.8 18.9 + - - -
308A VAL* 4.1 8.0 - - + +
310A HIS* 3.6 12.3 - - + +
320A TYR* 2.7 55.8 + - + +
321A TYR* 3.2 9.5 + - - -
323A GLU* 1.3 75.7 - - - +
325A GLY* 1.3 59.6 + - - +
326A ARG 3.2 0.4 - - - -
327A ALA* 3.0 29.6 + - - +
336A ALA* 3.6 27.0 - - + +
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Residues in contact with GLY 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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210A ARG* 2.9 28.7 + - - -
213A ILE* 4.1 4.9 - - - -
215A TYR* 5.9 0.2 - - - -
321A TYR* 2.9 22.7 + - - -
322A GLN 3.9 3.6 - - - -
323A GLU 3.1 1.2 - - - -
324A THR* 1.3 76.4 + - - +
326A ARG* 1.3 57.7 + - - +
327A ALA 3.2 1.2 + - - -
329A ARG* 2.8 25.0 + - - -
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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