Contacts of the helix formed by residues 289 - 299 (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 SER 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B TRP* 3.9 0.7 - - - +
287B SER* 3.3 15.9 + - - -
288B TYR* 1.3 80.5 - - - +
290B LEU* 1.3 65.0 + - - +
291B ASP* 4.0 6.6 + - - +
292B TYR* 3.0 27.2 + - - +
293B ILE* 3.0 12.5 + - - +
850B SER 5.5 1.6 - - - -
851B GLY 4.4 9.3 + - - -
852B THR* 5.8 4.0 - - - -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 5.0 7.4 - - - +
216B TRP* 3.5 41.0 - - + +
289B SER* 1.3 71.5 - - - +
291B ASP* 1.3 57.2 + - - +
293B ILE* 4.2 1.0 - - - +
294B SER* 3.0 32.4 + - - -
302B LYS* 4.2 21.3 - - + +
327B ALA* 3.6 39.3 - - + +
330B ARG* 4.5 11.0 - - + -
331B VAL* 3.6 28.5 - - + +
334B ILE* 4.7 7.2 - - + -
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Residues in contact with ASP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 3.1 6.5 - - - +
290B LEU* 1.3 78.3 - - - +
292B TYR* 1.3 62.6 + - - +
294B SER* 3.9 3.2 + - - -
295B GLU* 3.2 38.5 + - - +
301B GLY* 3.8 2.1 - - - -
302B LYS* 2.8 58.7 + - - +
851B GLY 6.0 2.0 - - - +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 3.3 34.8 + - + -
286B PRO* 2.8 31.8 - - + +
287B SER* 3.2 32.5 - - - +
289B SER* 3.0 21.6 + - - +
291B ASP* 1.3 77.6 - - - +
293B ILE* 1.3 65.0 + - - +
295B GLU* 3.3 14.3 + - + +
296B PHE* 3.1 21.6 + - + +
739B LYS* 3.5 23.0 - - - +
831B TYR* 4.4 12.6 - - - -
851B GLY* 4.2 13.4 + - - +
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.5 35.7 - - + -
277B TYR* 3.4 43.7 - - + +
285B GLN* 3.6 20.2 - - + -
287B SER 3.3 20.6 - - - +
288B TYR* 3.6 13.0 - - + -
289B SER 3.0 16.0 + - - +
290B LEU 4.2 2.0 - - - +
292B TYR* 1.3 77.5 - - - +
294B SER* 1.3 56.4 + - - +
296B PHE* 3.4 4.1 + - - +
297B GLU* 3.0 28.1 + - - +
334B ILE* 3.7 9.9 - - + -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU 3.0 20.8 + - - -
291B ASP* 3.9 0.9 + - - -
293B ILE* 1.3 74.3 - - - +
295B GLU* 1.3 57.1 + - - +
298B LEU* 2.9 40.6 + - - +
299B ASN 3.3 0.5 + - - -
300B VAL 2.7 25.4 + - - +
301B GLY* 3.2 18.7 + - - -
302B LYS* 4.8 0.2 - - - +
330B ARG* 4.3 15.6 - - - +
334B ILE* 4.0 17.2 - - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 3.2 31.9 + - - +
292B TYR* 3.3 15.9 + - - +
293B ILE 3.2 0.6 - - - -
294B SER* 1.3 76.9 + - - +
296B PHE* 1.3 61.0 + - - +
299B ASN* 3.1 27.5 + - - +
300B VAL* 3.4 19.2 - - - +
301B GLY* 4.3 6.6 + - - -
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Residues in contact with PHE 296 (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* 3.7 11.9 - - - -
283B THR* 5.1 10.8 - - + -
285B GLN* 3.4 32.5 - - - +
292B TYR* 3.1 15.8 + + + +
293B ILE* 3.5 9.2 - - - +
295B GLU* 1.3 80.9 - - - +
297B GLU* 1.3 89.4 + - + +
299B ASN* 3.8 8.5 - - - +
337B LYS* 4.7 1.7 + - - -
338B ARG* 4.6 5.8 - - - -
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 2.7 27.1 + - + +
293B ILE* 3.0 21.6 + - + +
296B PHE* 1.3 93.9 - - + +
298B LEU* 1.3 74.7 + - + +
299B ASN* 3.5 7.9 + - - -
334B ILE* 4.4 11.9 - - + -
337B LYS* 2.5 48.9 + - + +
338B ARG* 2.7 43.1 + - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B SER* 2.9 23.9 + - - +
297B GLU* 1.3 79.9 - - + +
299B ASN* 1.3 79.2 + - - +
300B VAL* 4.1 12.7 - - + +
330B ARG* 3.6 18.6 - - - +
333B GLN* 3.2 46.9 - - + +
334B ILE* 3.9 28.9 - - + +
337B LYS* 4.4 10.8 - - + -
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Residues in contact with ASN 299 (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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294B SER 3.3 0.4 + - - -
295B GLU* 3.1 22.2 + - - +
296B PHE 3.8 8.5 + - - +
297B GLU 3.9 9.6 + - - -
298B LEU* 1.3 84.3 + - - +
300B VAL* 1.3 64.4 + - - +
337B LYS* 5.5 0.4 - - - +
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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