Contacts of the helix formed by residues 314 - 327 (chain D) in PDB entry 5TJ4
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 ASP 314 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310D GLU 4.6 0.6 + - - -
311D LEU* 2.9 17.5 + - + +
312D ALA 3.6 6.6 - - - +
313D LYS* 1.3 78.0 - - - +
315D PRO* 1.4 73.2 - - - +
316D ARG* 2.7 67.9 + - - +
317D ILE* 3.4 14.1 + - + +
318D ALA* 3.4 16.6 + - - +
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Residues in contact with PRO 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D VAL 4.9 1.9 - - - +
313D LYS 3.5 6.7 - - - +
314D ASP* 1.4 90.6 - - - +
316D ARG* 1.3 60.7 + - + +
318D ALA* 3.4 9.3 + - + +
319D ALA* 3.0 26.2 + - - +
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Residues in contact with ARG 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TRP* 3.5 52.4 - - + +
236D ASP* 3.6 13.5 + - - -
242D TYR* 2.7 47.2 + - + -
244D VAL* 3.7 24.1 - - + +
298D PRO* 5.3 5.7 - - - +
314D ASP* 2.7 35.4 + - - +
315D PRO* 1.3 72.5 - - + +
317D ILE* 1.3 58.8 + - - +
319D ALA* 3.4 3.5 + - - +
320D THR* 3.0 29.6 + - - -
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Residues in contact with ILE 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TRP* 4.0 21.8 - - + -
294D ASN* 5.9 0.7 - - - +
298D PRO* 6.0 1.1 - - + -
300D GLY* 3.5 29.2 - - - +
301D ALA* 3.9 26.5 - - + +
308D GLU* 4.2 10.8 - - - +
311D LEU* 3.5 33.9 - - + +
312D ALA* 4.5 4.0 - - - -
314D ASP* 3.4 18.6 + - + +
315D PRO 3.3 0.4 - - - -
316D ARG* 1.3 74.5 - - - +
318D ALA* 1.3 59.0 + - - +
320D THR* 3.2 7.0 + - - +
321D MET* 2.9 33.8 + - - +
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ALA 5.0 6.2 + - - +
314D ASP 3.4 10.6 + - - +
315D PRO* 3.5 13.0 - - + +
316D ARG 3.3 0.4 - - - -
317D ILE* 1.3 79.8 - - - +
319D ALA* 1.3 56.6 + - - +
321D MET* 3.3 11.2 + - - +
322D GLU* 3.0 28.7 + - - +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D SER* 4.0 0.4 - - - -
244D VAL* 3.4 39.5 - - + +
245D THR* 4.0 9.4 - - - +
246D VAL* 4.9 0.7 - - - +
315D PRO 3.0 12.4 + - - +
316D ARG 3.5 8.7 - - - +
318D ALA* 1.3 73.1 - - - +
320D THR* 1.3 66.2 + - - +
322D GLU* 3.4 10.5 + - - +
323D ASN* 2.9 30.7 + - - -
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Residues in contact with THR 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 4.7 10.8 - - + +
112D ALA* 3.8 31.9 + - + +
114D SER* 3.2 18.9 + - - -
229D PRO* 4.2 11.8 - - + +
232D TRP* 3.6 17.1 - - - -
300D GLY* 5.2 0.2 - - - -
301D ALA* 5.1 7.6 - - + +
316D ARG 3.0 14.1 + - - -
317D ILE* 3.2 12.5 + - - +
319D ALA* 1.3 76.1 - - - +
321D MET* 1.3 59.5 + - + +
323D ASN* 3.2 5.8 + - - +
324D ALA* 2.8 27.3 + - + +
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Residues in contact with MET 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D ALA* 4.6 13.7 - - + -
308D GLU* 4.1 20.6 - - - +
312D ALA* 5.4 6.3 - - + -
317D ILE* 2.9 26.1 + - - +
318D ALA* 3.3 8.3 + - - +
320D THR* 1.3 76.5 - - + +
322D GLU* 1.3 57.8 + - - +
324D ALA* 3.6 9.6 - - + +
325D GLN* 2.9 29.5 + - - +
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D VAL* 3.2 27.4 - - + +
318D ALA 3.0 16.7 + - - +
319D ALA* 3.7 9.5 - - - +
320D THR 3.3 0.4 - - - -
321D MET* 1.3 75.2 - - - +
323D ASN* 1.3 62.6 + - - +
325D GLN* 3.4 13.0 + - - +
326D LYS* 3.1 50.6 + - - +
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Residues in contact with ASN 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA* 4.9 1.1 - - + -
113D LEU 3.4 20.6 - - - +
114D SER* 3.3 17.2 + - - +
245D THR 3.3 21.6 + - - -
246D VAL* 3.4 6.8 - - - +
247D LEU* 2.9 32.7 + - - +
255D SER 5.4 1.0 - - - +
257D PRO* 3.6 16.3 - - + +
319D ALA 2.9 22.2 + - - -
320D THR 3.5 5.8 - - - +
322D GLU* 1.3 72.0 - - - +
324D ALA* 1.3 64.2 + - - +
325D GLN 3.0 1.1 - - - -
326D LYS* 3.0 8.8 + - - +
327D GLY 2.9 19.6 + - - -
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 5.0 7.4 - - + -
112D ALA* 4.0 15.6 - - + +
259D VAL* 3.8 29.2 - - + +
320D THR* 2.8 19.5 + - + +
321D MET* 3.6 12.3 - - + +
323D ASN* 1.3 73.3 - - - +
325D GLN* 1.3 61.8 + - - +
327D GLY 3.3 18.0 + - - +
329D ILE 5.6 0.2 + - - -
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Residues in contact with GLN 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D MET 2.9 17.3 + - - +
322D GLU* 3.5 14.0 - - - +
323D ASN 3.0 0.2 - - - -
324D ALA* 1.3 78.9 - - - +
326D LYS* 1.3 92.5 + - - +
327D GLY 3.3 8.1 - - - +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 5.8 3.4 - - - +
246D VAL* 4.9 7.4 - - + +
254D PRO* 3.8 31.2 - - + +
255D SER 4.0 17.5 - - - +
256D LYS* 3.6 18.4 - - - +
322D GLU* 3.1 42.7 + - - +
323D ASN* 3.0 8.8 + - - +
325D GLN* 1.3 97.3 - - - +
327D GLY* 1.3 59.8 + - - +
328D GLU* 5.5 0.3 - - - +
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Residues in contact with GLY 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D LYS* 3.7 14.8 - - - -
257D PRO* 3.4 19.0 - - - +
259D VAL* 4.6 0.2 - - - -
323D ASN 2.9 11.5 + - - -
324D ALA 3.3 15.1 - - - +
325D GLN 3.2 8.9 - - - +
326D LYS* 1.3 78.6 - - - +
328D GLU* 1.3 69.3 + - - +
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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