Contacts of the helix formed by residues 250 - 261 (chain D) in PDB entry 5MR4
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 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D PRO* 1.3 75.9 - - - +
251D CYS* 1.3 65.4 + - - +
252D LEU* 3.1 32.9 + - - +
253D ASP* 3.0 27.8 + - - +
254D LEU* 3.0 19.9 + - - +
324D SER 3.2 14.2 + - - -
325D CYS* 3.7 1.4 - - - +
326D ARG 3.1 24.0 + - - +
327D GLY 4.2 8.3 - - - +
328D SER* 3.0 33.5 + - - +
335D CYS* 3.9 2.2 - - - -
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Residues in contact with CYS 251 (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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249D PRO 3.8 0.2 + - - -
250D ASN* 1.3 71.9 - - - +
252D LEU* 1.3 59.6 + - - +
254D LEU* 3.3 3.4 + - - +
255D ARG* 2.8 27.7 + - - +
323D CYS* 2.1 50.0 - - - -
324D SER* 2.9 28.3 + - - -
335D CYS* 3.7 15.0 - - - +
338D PHE* 3.9 22.4 - - + -
339D LEU* 3.8 19.5 - - - -
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Residues in contact with LEU 252 (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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250D ASN* 3.1 10.0 + - - +
251D CYS* 1.3 74.4 - - - +
253D ASP* 1.3 62.7 + - - +
255D ARG* 3.4 38.5 + - - +
256D GLY* 2.9 24.4 + - - -
331D MET* 3.4 43.1 - - + -
334D GLU* 4.1 12.3 - - - +
335D CYS* 3.9 33.2 - - + +
338D PHE* 4.3 12.8 - - + -
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Residues in contact with ASP 253 (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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249D PRO* 4.9 5.8 - - + +
250D ASN* 3.0 33.7 + - + +
252D LEU* 1.3 77.1 - - - +
254D LEU* 1.3 63.3 + - - +
256D GLY* 3.0 4.5 + - - -
257D VAL* 3.0 29.4 + - + +
327D GLY 5.6 0.3 - - - +
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Residues in contact with LEU 254 (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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249D PRO* 4.2 17.6 - - + +
250D ASN 3.0 11.6 + - - +
251D CYS* 3.6 10.1 - - - +
253D ASP* 1.3 73.6 - - - +
255D ARG* 1.3 59.4 + - - +
257D VAL* 3.2 10.7 + - + +
258D CYS* 2.9 27.7 + - - +
304D ASP* 3.6 37.7 - - + +
305D MET* 4.0 22.0 - - - -
321D PRO* 4.3 6.3 - - + -
322D TRP* 3.5 28.0 - - + +
323D CYS* 3.9 8.7 - - + -
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Residues in contact with ARG 255 (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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120D GLU* 3.2 21.8 + - - +
122D PHE* 3.6 27.8 + - - +
251D CYS 2.8 14.8 + - - +
252D LEU* 3.5 29.9 + - - +
254D LEU* 1.3 75.4 - - - +
256D GLY* 1.3 58.3 + - - +
258D CYS* 3.2 1.2 + - - +
259D ARG* 2.8 74.3 + - - +
268D LEU* 4.1 9.4 - - + -
272D HIS* 5.6 0.2 - - - -
305D MET* 3.6 12.7 - - + +
334D GLU* 3.0 29.1 + - - -
338D PHE* 3.6 28.6 - - + -
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Residues in contact with GLY 256 (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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252D LEU 2.9 14.7 + - - -
253D ASP* 3.0 5.5 + - - -
255D ARG* 1.3 78.5 - - - +
257D VAL* 1.3 60.7 + - - +
259D ARG* 3.3 12.3 + - - +
260D THR* 3.3 18.4 + - - +
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Residues in contact with VAL 257 (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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253D ASP* 3.0 18.8 + - + +
254D LEU* 3.7 13.0 - - + +
256D GLY* 1.3 75.6 - - - +
258D CYS* 1.3 63.8 + - - +
260D THR* 2.8 29.6 + - - +
261D ASP* 3.7 2.4 + - - +
304D ASP* 3.7 26.3 - - + +
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Residues in contact with CYS 258 (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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254D LEU 2.9 16.8 + - - +
255D ARG 3.2 4.9 + - - +
257D VAL* 1.3 77.5 - - - +
259D ARG* 1.3 57.1 + - + +
261D ASP* 3.1 25.8 + - - +
264D CYS* 2.1 63.3 - - - +
265D ARG* 3.4 3.1 + - - -
268D LEU* 4.2 12.6 - - - -
304D ASP* 4.2 8.5 + - + +
305D MET* 3.6 24.9 - - + -
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Residues in contact with ARG 259 (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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120D GLU* 3.8 17.7 + - - +
121D GLU 2.7 26.6 + - - -
122D PHE 3.4 16.2 + - - -
124D GLU* 3.4 40.9 + - - +
255D ARG* 2.8 67.1 + - + +
256D GLY* 3.3 6.3 + - - +
257D VAL 3.3 0.2 - - - -
258D CYS* 1.3 76.4 - - - +
260D THR* 1.3 58.6 + - - +
261D ASP 3.3 0.6 + - - +
265D ARG* 3.4 40.2 + - + +
268D LEU* 4.5 17.1 - - + +
272D HIS* 4.8 3.8 + - - -
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Residues in contact with THR 260 (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 GLY 3.3 17.7 + - - +
257D VAL* 2.8 21.6 + - - +
259D ARG* 1.3 76.5 - - - +
261D ASP* 1.3 60.5 + - - +
262D HIS* 4.0 7.4 + - - -
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Residues in contact with ASP 261 (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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103D LEU* 6.1 1.5 - - - +
257D VAL 4.6 4.0 - - - +
258D CYS 3.1 9.1 + - - +
259D ARG 4.5 0.9 - - - -
260D THR* 1.3 82.9 + - - +
262D HIS* 1.3 66.1 + - - +
263D LEU* 3.1 13.4 + - - +
264D CYS* 2.9 32.3 + - + +
265D ARG* 3.0 27.2 + - - +
303D PHE* 4.5 4.5 - - - -
304D ASP* 4.7 8.3 - - - +
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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