Contacts of the helix formed by residues 289 - 299 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C TRP* 4.6 0.2 - - - +
287C SER* 3.3 10.7 + - - -
288C TYR* 1.3 80.7 - - - +
290C LEU* 1.3 65.9 + - - +
291C ASP* 3.6 7.3 + - - +
292C TYR* 2.9 25.3 + - - +
293C ILE* 3.1 16.5 + - - +
850C SER 5.4 1.3 - - - -
851C GLY 4.6 7.3 + - - -
852C THR* 6.0 3.4 - - - -
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 3.6 53.1 - - + +
288C TYR 3.6 1.8 + - - -
289C SER* 1.3 72.3 - - - +
291C ASP* 1.3 51.0 + - - +
294C SER* 2.5 40.1 + - - +
302C LYS* 5.8 0.9 - - - +
327C ALA* 3.4 39.3 - - + +
330C ARG* 4.2 12.8 - - + -
331C VAL* 4.0 12.6 - - + -
334C ILE* 3.7 20.2 - - + -
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Residues in contact with ASP 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C SER* 3.0 7.3 + - - +
290C LEU* 1.3 78.2 - - - +
292C TYR* 1.3 62.0 + - - +
294C SER* 2.8 14.9 + - - -
295C GLU* 3.0 15.2 + - - +
301C GLY* 3.1 17.8 - - - -
302C LYS* 3.4 34.9 + - + +
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Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLN* 3.5 25.4 + - - -
286C PRO* 3.6 27.0 - - + +
287C SER* 3.5 27.4 - - - +
289C SER* 2.9 21.8 + - - +
291C ASP* 1.3 77.1 - - - +
293C ILE* 1.3 61.0 + - + +
295C GLU* 3.3 6.8 + - + +
296C PHE* 3.0 30.7 + + + +
739C LYS* 3.7 22.2 - - - +
831C TYR* 4.1 16.6 - - - -
851C GLY* 3.7 22.9 + - - +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C TRP* 3.5 37.0 - - + -
277C TYR* 3.8 32.8 - - + +
285C GLN* 3.6 30.3 - - + -
287C SER 3.5 21.1 - - - +
288C TYR* 3.9 8.3 - - + -
289C SER 3.1 15.0 + - - +
290C LEU 4.2 1.6 - - - +
292C TYR* 1.3 77.2 - - + +
294C SER* 1.3 58.7 + - - +
296C PHE* 3.3 3.3 + - + +
297C GLU* 2.9 28.7 + - + +
334C ILE* 4.1 9.9 - - + -
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 2.5 25.4 + - - +
291C ASP* 2.8 18.0 + - - -
293C ILE* 1.3 73.2 - - - +
295C GLU* 1.3 57.8 + - - +
298C LEU* 2.7 36.5 + - - +
300C VAL 3.0 14.6 - - - +
301C GLY* 3.5 9.2 - - - -
330C ARG* 4.1 23.0 - - - +
334C ILE* 3.9 18.8 - - - +
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Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ASP* 3.0 22.2 + - - +
292C TYR* 3.6 7.2 - - + +
294C SER* 1.3 78.2 + - - +
296C PHE* 1.3 59.5 + - - +
299C ASN* 3.1 26.4 + - - +
300C VAL* 2.7 42.5 + - - +
301C GLY 3.6 2.1 + - - +
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Residues in contact with PHE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C TYR* 3.7 11.9 - - - -
283C THR* 5.1 10.1 - - + -
285C GLN* 3.3 32.5 - - - +
292C TYR* 3.0 24.7 + + + +
293C ILE* 3.5 6.3 - - - +
294C SER 3.2 0.2 - - - -
295C GLU* 1.3 80.7 - - - +
297C GLU* 1.3 84.3 - - + +
299C ASN* 4.4 6.1 - - - +
337C LYS* 5.1 1.3 + - - -
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Residues in contact with GLU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TYR* 2.8 38.8 + - + +
293C ILE* 2.9 21.7 + - + +
296C PHE* 1.3 95.5 - - + +
298C LEU* 1.3 74.2 + - + +
299C ASN* 4.2 4.4 - - - +
334C ILE* 4.5 10.1 - - + -
337C LYS* 3.0 55.8 + - + +
338C ARG* 3.5 28.2 + - - -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C SER* 2.7 27.0 + - - +
297C GLU* 1.3 84.5 - - + +
299C ASN* 1.3 70.9 + - - +
300C VAL* 3.7 14.4 - - + +
330C ARG* 3.8 20.4 - - - +
333C GLN* 3.4 57.9 - - + +
334C ILE* 3.9 13.7 - - + +
337C LYS* 4.6 10.3 - - + -
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Residues in contact with ASN 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C GLU* 3.1 26.9 + - - -
296C PHE 4.4 6.2 - - - +
297C GLU 4.2 6.6 - - - +
298C LEU* 1.3 80.2 - - - +
300C VAL* 1.3 66.1 + - - +
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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