Contacts of the helix formed by residues 265 - 270 (chain D) in PDB entry 7CHW
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 LEU 265 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D LEU* 4.1 20.4 - - + -
249D LEU 5.4 0.9 - - - +
250D ARG* 4.2 15.3 - - + -
263D SER* 2.8 8.8 + - - +
264D ASP* 1.3 77.1 - - - +
266D ASN* 1.3 61.0 + - - +
267D ASP 3.3 1.1 - - - -
268D LEU* 3.8 9.1 + - + +
269D TYR* 3.0 41.3 + - + -
306D LEU* 4.0 26.5 - - + -
325D LYS 4.2 12.1 - - - +
327D LEU* 3.9 28.7 - - + +
330D MET* 3.7 28.9 - - + -
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Residues in contact with ASN 266 (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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43D THR* 5.4 2.2 - - + +
56D LEU* 4.4 9.3 - - + +
57D PHE* 3.4 31.8 - - + -
250D ARG* 3.3 40.7 + - - -
251D PRO 3.9 3.4 + - - -
252D LEU* 4.6 0.8 - - - +
262D THR* 3.1 28.1 + - - +
263D SER* 4.1 3.4 - - - +
264D ASP* 3.3 1.0 - - - +
265D LEU* 1.3 78.2 - - - +
267D ASP* 1.3 63.5 + - - +
269D TYR* 4.1 4.7 - - - +
270D ARG* 3.2 31.4 + - - +
449F THR* 5.1 10.5 - - + -
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Residues in contact with ASP 267 (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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262D THR* 5.1 4.0 + - - +
263D SER 4.6 6.1 - - - +
264D ASP* 4.0 9.2 + - - +
265D LEU 3.3 0.4 - - - -
266D ASN* 1.3 85.3 - - - +
268D LEU* 1.3 62.6 + - - +
269D TYR 3.4 0.4 - - - -
270D ARG* 3.9 20.5 + - - +
271D ARG* 3.4 33.5 + - - +
317D THR* 4.3 12.8 + - - -
318D GLY* 4.6 10.4 + - - +
324D LEU* 4.1 23.2 - - + +
449F THR* 4.4 8.8 + - - +
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Residues in contact with LEU 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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264D ASP 3.9 12.8 - - - +
265D LEU* 3.8 11.2 + - + +
266D ASN 3.5 0.2 - - - -
267D ASP* 1.3 77.2 - - - +
269D TYR* 1.3 60.2 + - - +
270D ARG 3.4 0.2 - - - -
271D ARG* 3.9 21.2 - - - +
272D VAL* 3.1 29.3 + - - +
302D ALA 4.7 2.7 - - - +
305D ALA* 3.9 29.8 - - + +
306D LEU* 4.0 20.6 - - + +
309D ASN* 4.7 6.3 - - - +
324D LEU* 3.3 36.6 - - + -
325D LYS 4.2 3.4 - - - +
326D SER* 3.9 22.7 - - - +
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Residues in contact with TYR 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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1332C SER* 3.2 22.9 + - - -
56D LEU* 4.0 22.2 - - + -
105D ILE* 4.4 14.4 - - + -
242D LEU* 4.7 4.0 - - + -
243D PRO 3.5 5.0 + - - -
244D VAL* 3.4 28.3 - - + -
245D LEU* 3.3 17.0 + - + +
250D ARG* 4.1 26.2 - - - -
265D LEU* 3.0 43.0 + - + +
266D ASN* 4.7 0.2 - - - -
268D LEU* 1.3 74.8 - - - +
270D ARG* 1.3 60.3 + - - +
271D ARG 3.1 5.1 + - - -
272D VAL* 3.7 2.5 + - + +
273D ILE* 3.0 32.9 + - - +
306D LEU* 3.9 26.0 - - + +
327D LEU* 4.2 4.7 - - - +
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Residues in contact with ARG 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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41D PRO* 3.3 42.7 - - + +
43D THR* 4.8 5.2 - - - -
56D LEU* 4.2 6.5 - - + +
266D ASN 3.2 30.8 + - - +
267D ASP* 3.8 18.9 + - - +
268D LEU 3.4 0.2 - - - -
269D TYR* 1.3 77.9 - - - +
271D ARG* 1.3 52.2 + - - +
273D ILE* 4.1 2.2 - - - -
274D ASN* 2.5 44.3 + - - +
398F GLY 5.9 0.6 + - - -
446F GLN* 5.0 6.1 + - - +
447F ALA* 4.2 22.6 + - - +
448F ARG 3.9 20.3 + - - -
449F THR* 3.7 29.0 + - - +
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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