Contacts of the helix formed by residues 267 - 279 (chain D) in PDB entry 5TT2
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 SER 267 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D PRO* 1.3 76.7 - - - +
268D PRO* 1.3 75.6 - - - +
269D ILE* 3.5 11.2 + - - +
270D ASP* 3.1 30.9 + - - -
271D CYS* 3.0 22.6 + - - -
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Residues in contact with PRO 268 (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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84D ASN* 6.1 5.6 - - + +
86D THR* 3.5 25.1 - - - +
266D PRO 4.4 2.2 - - - +
267D SER* 1.3 88.7 - - - +
269D ILE* 1.3 60.9 + - + +
271D CYS* 3.4 7.1 + - + -
272D TYR* 3.0 25.8 + - - +
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Residues in contact with ILE 269 (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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267D SER* 3.2 10.0 - - - +
268D PRO* 1.3 76.3 - - + +
270D ASP* 1.3 66.5 + - - +
272D TYR* 3.3 9.3 + - + +
273D LEU* 3.0 45.8 + - + +
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Residues in contact with ASP 270 (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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238D ASP 4.0 17.2 - - - +
239D VAL* 4.0 5.6 - - + +
240D VAL* 4.0 20.2 + - - +
241D MET* 3.5 15.4 - - + +
266D PRO* 3.9 4.7 - - + +
267D SER* 3.1 33.0 + - - +
269D ILE* 1.3 79.5 - - - +
271D CYS* 1.3 56.8 + - - +
273D LEU* 3.8 5.3 - - - +
274D CYS* 2.9 32.7 + - - +
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Residues in contact with CYS 271 (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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86D THR* 3.8 17.7 - - + +
87D ARG* 3.5 36.1 - - - +
90D LEU* 3.7 10.4 - - + +
241D MET* 3.5 10.1 - - - -
266D PRO* 3.6 24.2 - - - -
267D SER 3.0 20.0 + - - -
268D PRO* 3.6 9.0 - - - +
269D ILE 3.3 0.2 - - - -
270D ASP* 1.3 76.9 - - - +
272D TYR* 1.3 56.6 + - - +
274D CYS* 3.7 1.2 - - - +
275D ASN* 3.0 31.4 + - - +
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Residues in contact with TYR 272 (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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86D THR* 3.5 16.0 - - + +
268D PRO 3.0 17.8 + - - +
269D ILE* 3.6 9.6 - - + +
271D CYS* 1.3 77.0 - - - +
273D LEU* 1.3 79.1 + - + +
275D ASN* 3.2 7.7 + - + +
276D ARG* 2.9 51.7 + - + +
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Residues in contact with LEU 273 (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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234D ASN* 4.4 6.2 + - - -
237D SER* 5.4 9.7 + - - -
238D ASP 5.5 9.0 - - - +
239D VAL* 4.8 15.7 - - + +
269D ILE* 3.0 40.7 + - + +
270D ASP* 4.1 4.9 - - - +
272D TYR* 1.3 96.7 - - + +
274D CYS* 1.3 59.7 + - - +
276D ARG* 3.5 12.0 + - - +
277D GLY* 3.1 18.9 + - - -
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Residues in contact with CYS 274 (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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90D LEU* 4.0 16.4 - - + -
229D ALA* 5.1 5.8 - - - -
239D VAL* 3.7 19.0 - - + +
241D MET* 3.7 27.6 - - + -
243D LEU* 4.4 14.1 - - - -
270D ASP 2.9 19.3 + - - +
271D CYS 3.7 3.1 - - - +
273D LEU* 1.3 74.7 - - - +
275D ASN* 1.3 65.9 + - - +
277D GLY* 3.1 11.3 + - - -
278D LEU* 3.1 26.0 + - - +
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Residues in contact with ASN 275 (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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41D ALA 4.4 8.0 - - - +
44D VAL 5.0 1.0 + - - -
46D GLN* 4.1 25.2 + - - +
86D THR* 4.7 3.0 + - + +
89D CYS* 3.9 12.5 + - - +
90D LEU* 3.6 41.5 - - + +
93D ALA* 4.3 13.0 - - - +
271D CYS 3.0 18.2 + - - +
272D TYR* 3.5 8.5 - - + +
274D CYS* 1.3 76.1 - - - +
276D ARG* 1.3 63.3 + - - +
278D LEU* 3.3 19.0 + - - +
279D LYS* 3.6 10.4 - - - +
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Residues in contact with ARG 276 (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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234C ASN* 2.9 35.6 + - - +
235C GLY* 2.6 28.6 + - - -
237C SER* 3.4 20.0 - - - -
363C PHE* 4.6 11.2 - - + -
234D ASN* 5.8 1.6 - - - +
272D TYR* 2.9 45.2 + - + +
273D LEU* 3.7 14.4 - - + +
275D ASN* 1.3 78.4 - - - +
277D GLY* 1.3 62.7 + - - +
279D LYS* 3.3 31.1 + - + +
280D THR* 4.4 2.8 + - - +
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Residues in contact with GLY 277 (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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234D ASN* 3.3 31.2 - - - -
273D LEU 3.1 11.2 + - - -
274D CYS* 3.1 4.6 + - - -
276D ARG* 1.3 77.3 - - - +
278D LEU* 1.3 61.5 + - - +
279D LYS 3.2 0.7 + - - -
280D THR* 3.2 10.7 + - - -
284D ARG* 2.8 26.3 + - - -
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Residues in contact with LEU 278 (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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37D PHE* 5.6 0.3 - - - -
41D ALA* 3.6 16.5 - - + +
90D LEU* 3.9 14.1 - - + -
93D ALA* 4.7 7.0 - - + -
94D VAL* 3.6 30.7 - - + -
97D LEU* 4.1 22.1 - - + +
212D PRO* 6.6 0.4 - - + -
227D TYR* 5.6 10.3 - - + -
243D LEU* 5.7 2.7 - - + -
274D CYS* 3.1 22.5 + - - +
275D ASN* 3.4 14.1 - - - +
276D ARG 3.2 0.4 - - - -
277D GLY* 1.3 77.3 - - - +
279D LYS* 1.3 61.7 + - - +
280D THR 3.0 1.8 + - - -
281D LEU* 3.1 36.6 + - + +
282D HIS* 4.7 1.2 + - - -
284D ARG* 4.9 0.4 - - - +
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Residues in contact with LYS 279 (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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363C PHE* 3.9 28.6 - - + -
364C GLU* 4.6 10.6 + - - +
399C LEU* 4.9 1.7 - - - +
41D ALA* 3.4 24.9 - - - +
42D ILE* 3.4 38.7 + - + +
46D GLN* 3.4 36.1 - - - +
275D ASN* 3.6 17.0 - - - +
276D ARG* 3.5 19.5 - - - +
277D GLY 3.2 0.6 - - - -
278D LEU* 1.3 77.0 - - - +
280D THR* 1.3 61.4 + - - +
281D LEU 3.6 0.2 - - - -
282D HIS* 3.1 20.6 - - - -
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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