Contacts of the helix formed by residues 272 - 281 (chain B) in PDB entry 3RMD
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 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLY 3.4 5.3 - - - +
217B ASN* 2.6 36.8 + - - -
218B VAL* 3.5 14.2 + - + -
219B GLU* 3.1 36.8 + - + +
220B SER* 4.1 4.5 + - - -
270B VAL* 3.7 5.2 + - + +
271B LEU* 1.3 69.9 - - - +
273B TYR* 1.3 61.6 + - - +
274B ILE* 3.0 20.2 + - - +
275B ASP* 2.8 39.6 + - - +
276B LEU* 3.0 9.2 + - - +
359B PHE* 5.5 0.8 - - - -
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Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASN* 6.0 0.2 - - - -
214B THR* 3.6 14.8 - - + +
215B GLY 2.9 23.2 + - - +
216B TRP* 3.7 23.6 - + + -
271B LEU 3.1 4.4 + - - -
272B ASP* 1.3 71.4 - - - +
274B ILE* 1.3 54.4 + - - +
275B ASP 3.2 0.2 - - - -
276B LEU* 3.6 15.9 - - + -
277B TYR* 2.7 39.6 + - + +
331B VAL* 3.9 14.4 - - + -
334B ILE* 3.9 19.1 - - + -
335B ASP* 2.8 51.2 + - + +
338B ARG* 3.9 0.2 - - - +
340B PHE* 3.2 39.9 + + + +
341B ILE* 3.7 15.5 - - + -
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B TRP* 3.3 41.8 - - + +
217B ASN* 3.9 25.1 - - - +
220B SER* 5.7 0.9 - - - +
272B ASP* 3.0 34.6 + - - +
273B TYR* 1.3 77.0 - - - +
275B ASP* 1.3 79.8 + - - +
277B TYR* 3.6 3.1 - - - +
278B LYS* 3.0 42.0 + - - +
288B TYR* 3.4 28.7 - - + +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B GLU* 4.1 13.5 - - - +
272B ASP* 2.8 22.3 + - + +
274B ILE* 1.3 94.7 - - - +
276B LEU* 1.3 66.8 + - - +
278B LYS* 3.7 10.8 + - - +
279B LYS* 2.8 25.8 + - - +
359B PHE* 3.8 19.0 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 3.6 37.0 - - + +
272B ASP 3.0 11.0 + - - +
273B TYR* 3.6 35.4 - - + +
275B ASP* 1.3 74.1 - - - +
277B TYR* 1.3 65.5 + - - +
279B LYS* 2.8 15.9 + - - +
280B PHE* 2.9 31.3 + - + +
340B PHE* 4.5 14.1 - - + -
341B ILE* 4.2 12.6 - - + +
344B SER* 3.6 22.2 - - - +
358B VAL* 5.4 0.4 - - + -
359B PHE* 3.7 19.5 - - + -
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.6 22.9 - + + -
273B TYR* 2.7 23.8 + - + +
274B ILE 3.6 3.8 - - - +
276B LEU* 1.3 73.3 - - - +
278B LYS* 1.3 56.9 + - - +
281B SER* 2.8 57.0 + - - -
283B THR* 4.4 2.4 - - + +
285B GLN* 3.8 10.9 + - - -
288B TYR* 3.7 22.7 - + - -
293B ILE* 3.4 38.3 - - + +
296B PHE* 3.7 12.6 - - - -
297B GLU* 2.7 33.8 + - + -
334B ILE* 4.4 9.9 - - + -
338B ARG* 4.3 4.0 - - - -
340B PHE* 4.0 20.7 - + - -
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Residues in contact with LYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ILE* 3.0 34.1 + - + +
275B ASP* 3.8 12.0 + - - +
276B LEU 3.3 0.2 - - - -
277B TYR* 1.3 76.8 - - - +
279B LYS* 1.3 60.1 + - - +
281B SER* 4.6 2.3 + - - -
282B PHE 5.0 3.8 + - - -
288B TYR* 3.4 64.0 - - + +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ASP 2.8 17.9 + - - +
276B LEU 2.8 5.8 + - - +
278B LYS* 1.3 78.3 - - - +
280B PHE* 1.3 88.0 + - + +
281B SER 3.7 0.2 - - - -
282B PHE* 4.2 15.8 + - - -
358B VAL 4.8 2.9 - - - -
359B PHE* 3.1 53.1 + - + +
361B PRO* 5.0 1.3 - - - +
2G G 2.9 47.2 + - - +
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B LEU* 2.9 28.6 + - + +
279B LYS* 1.3 101.6 - - + +
281B SER* 1.3 63.6 + - - +
282B PHE* 3.3 23.0 - + + -
338B ARG* 5.0 1.7 + - - -
340B PHE* 3.2 37.5 - + + -
343B LEU* 4.0 20.4 - - + -
344B SER* 4.2 19.1 - - - -
347B MET* 6.5 0.9 - - + -
358B VAL* 4.7 22.7 - - + -
359B PHE* 5.4 0.4 - + - -
561B LEU* 4.0 36.3 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B TYR* 2.8 42.9 + - - -
278B LYS* 5.0 1.6 - - - -
279B LYS 3.7 0.2 - - - -
280B PHE* 1.3 75.8 - - - +
282B PHE* 1.3 74.5 + - - +
283B THR* 3.2 22.5 - - - +
338B ARG* 2.9 35.6 + - - +
340B PHE* 3.8 8.8 - - - -
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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