Contacts of the helix formed by residues 1271 - 1279 (chain C) in PDB entry 5MS0
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 GLY1271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1269C ARG 3.7 4.8 + - - -
1270C PHE* 1.3 79.2 - - - +
1272C GLU* 1.3 64.1 + - - -
1273C MET 3.4 2.5 - - - -
1274C GLU* 3.3 12.5 + - - +
1275C VAL* 3.1 18.0 + - - +
343D LEU 3.9 1.3 + - - -
344D GLY* 3.8 10.1 - - - -
18J C 3.3 25.9 - - - -
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Residues in contact with GLU1272 (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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1271C GLY* 1.3 70.5 - - - -
1273C MET* 1.3 61.0 + - - +
1275C VAL* 2.9 24.7 + - + +
1276C TRP* 3.0 14.4 + - - +
342D LEU* 3.9 28.8 + - + +
18J C 3.9 2.8 + - - -
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Residues in contact with MET1273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271C GLY 3.4 0.2 - - - -
1272C GLU* 1.3 78.6 - - - +
1274C GLU* 1.3 60.4 + - - +
1276C TRP* 3.4 7.9 + - - +
1277C ALA* 3.2 18.0 + - - +
426D ALA 5.0 3.6 - - - +
428D THR* 3.2 42.5 - - - +
793D SER 6.0 0.4 - - - +
794D GLY* 5.7 9.0 - - - -
797D THR* 6.0 6.1 - - - -
17J G 5.8 7.3 + - + +
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Residues in contact with GLU1274 (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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1270C PHE* 4.6 7.0 - - + -
1271C GLY* 3.3 22.2 + - - +
1272C GLU 3.2 0.2 - - - -
1273C MET* 1.3 77.6 - - - +
1275C VAL* 1.3 63.6 + - - +
1277C ALA* 3.5 13.3 + - - +
1278C LEU* 3.7 12.8 + - - +
428D THR* 4.1 8.1 - - - -
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Residues in contact with VAL1275 (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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1271C GLY 3.1 8.6 + - - +
1272C GLU* 2.9 19.0 + - + +
1274C GLU* 1.3 77.6 - - - +
1276C TRP* 1.3 55.8 + - - +
1277C ALA 3.2 0.2 - - - -
1278C LEU* 3.7 2.3 + - - +
1279C GLU* 2.8 33.3 + - + +
1287C LEU* 5.4 4.8 - - - +
1351D VAL* 5.5 10.5 - - + -
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Residues in contact with TRP1276 (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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1272C GLU 3.0 12.6 + - - +
1273C MET* 3.4 8.5 + - - +
1274C GLU 3.4 0.2 - - - -
1275C VAL* 1.3 76.5 - - - +
1277C ALA* 1.3 51.0 + - - +
1279C GLU* 3.7 8.3 - - + -
1280C ALA* 2.7 35.3 + - - +
430D HIS 5.4 1.3 - - - +
801D VAL* 6.0 4.3 - - + -
917D VAL* 4.8 16.7 - - + +
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Residues in contact with ALA1277 (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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1273C MET 3.2 14.0 + - - +
1274C GLU* 3.8 8.5 - - - +
1275C VAL 3.2 1.2 - - - -
1276C TRP* 1.3 76.4 - - - +
1278C LEU* 1.3 61.7 + - - +
1280C ALA* 3.1 6.7 + - - +
1281C TYR* 2.9 26.0 + - - +
428D THR* 5.1 3.6 - - - -
430D HIS 4.6 9.0 - - - +
431D ARG* 4.0 19.0 - - - +
434D ILE* 4.0 27.6 - - + +
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Residues in contact with LEU1278 (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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1274C GLU 3.7 10.0 + - - +
1275C VAL 4.5 0.7 - - - +
1277C ALA* 1.3 77.8 - - - +
1279C GLU* 1.3 62.2 + - - +
1281C TYR* 3.2 23.4 + - - +
1283C ALA* 3.4 22.7 - - + +
1286C THR* 5.4 2.9 - - - -
1287C LEU* 3.7 29.6 - - + +
434D ILE* 5.4 1.4 - - - +
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Residues in contact with GLU1279 (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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1275C VAL 2.8 22.8 + - - +
1276C TRP* 3.7 8.5 - - + -
1278C LEU* 1.3 77.1 - - - +
1280C ALA* 1.3 60.0 + - - +
1281C TYR 3.3 7.8 - - - +
1283C ALA 5.4 0.2 - - - -
1287C LEU* 4.8 4.9 - - + +
914D ALA* 4.2 17.6 + - + +
917D VAL* 6.1 1.3 - - - -
1347D LEU* 4.9 20.9 - - + +
1359D ALA* 5.7 2.8 - - - +
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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