Contacts of the helix formed by residues 1044 - 1051 (chain D) in PDB entry 3CMT
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 SER1044 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1042D THR* 3.0 18.7 + - - -
1043D GLY* 1.3 79.4 - - - +
1045D LEU* 1.3 61.7 + - - +
1047D LEU* 3.1 26.1 + - - -
1048D ASP* 3.1 16.1 + - - -
1260D PHE* 3.3 23.6 - - - -
1268D ILE* 4.0 12.3 - - - -
1270D PHE* 4.3 0.7 - - - -
1273D GLU* 2.5 28.1 + - - -
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Residues in contact with LEU1045 (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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1044D SER* 1.3 71.2 - - - +
1046D SER* 1.3 59.3 + - - +
1048D ASP* 3.1 7.7 + - - +
1049D ILE* 3.0 35.5 + - + +
1270D PHE* 3.5 19.8 - - + +
1273D GLU* 3.0 15.7 + - + +
1274D LEU* 3.7 40.8 - - + +
1277D LEU* 4.2 18.8 - - + -
1320D GLU* 3.7 28.3 - - + +
1323D VAL* 4.2 9.4 - - + -
1324D ARG* 3.8 26.7 - - + +
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Residues in contact with SER1046 (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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1044D SER* 3.5 0.9 + - - -
1045D LEU* 1.3 78.4 - - - +
1047D LEU* 1.3 57.0 + - - +
1049D ILE* 3.4 13.4 + - - +
1050D ALA* 2.9 27.2 + - - +
1257D GLN 4.7 0.9 - - - +
1258D ALA* 3.4 19.8 - - - +
1259D GLU 3.5 16.2 + - - -
1260D PHE* 4.1 0.7 - - - -
1273D GLU* 2.6 23.7 + - - -
1277D LEU* 4.2 18.2 - - - -
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Residues in contact with LEU1047 (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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1042D THR* 3.5 31.4 - - + +
1044D SER* 3.1 20.2 + - - +
1046D SER* 1.3 74.0 + - - +
1048D ASP* 1.3 56.4 - - - +
1049D ILE 3.1 1.6 - - - -
1050D ALA* 3.0 4.2 + - + -
1051D LEU* 2.7 51.1 + - + +
1075D LEU* 4.0 24.5 - - + -
1223D LEU* 4.5 12.8 - - + -
1244D VAL* 4.3 27.1 - - + +
1246D VAL* 4.3 13.0 - - + -
1258D ALA* 3.5 14.1 - - + +
1260D PHE* 4.8 0.2 - - + -
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Residues in contact with ASP1048 (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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1041D SER* 3.0 21.2 + - - -
1042D THR* 2.9 32.2 + - - +
1044D SER 3.1 16.3 + - - +
1045D LEU* 3.1 9.2 + - - +
1047D LEU* 1.3 75.4 - - - +
1049D ILE* 1.3 60.2 + - + +
1051D LEU* 3.6 2.8 + - - +
1052D GLY 3.6 4.3 + - - -
1054D GLY* 3.1 44.1 + - - +
1055D GLY* 3.4 8.2 - - - +
1270D PHE* 5.5 0.5 - - - -
1324D ARG* 2.7 33.6 + - - +
1328D LEU* 3.4 2.9 - - - +
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Residues in contact with ILE1049 (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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1045D LEU* 3.0 40.1 + - + +
1046D SER* 3.6 13.9 - - - +
1047D LEU 3.1 0.2 - - - -
1048D ASP* 1.3 75.2 - - + +
1050D ALA* 1.3 61.7 + - - +
1052D GLY* 2.9 21.3 + - - -
1256D LYS* 4.2 9.2 + - + +
1277D LEU* 4.1 15.7 - - + -
1323D VAL* 4.1 21.8 - - + +
1324D ARG* 5.4 3.1 - - + -
1327D LEU* 3.8 37.3 - - + +
1328D LEU* 3.6 15.7 - - + +
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Residues in contact with ALA1050 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1046D SER 2.9 18.0 + - - +
1047D LEU* 3.4 9.2 - - + +
1049D ILE* 1.3 75.5 - - - +
1051D LEU* 1.3 61.4 + - - +
1052D GLY* 3.1 1.4 + - - -
1246D VAL* 4.1 17.8 - - + +
1249D ASN* 4.8 0.2 + - - -
1253D ALA 4.3 5.7 - - - +
1256D LYS* 3.4 36.2 - - + +
1257D GLN 3.9 27.4 - - - +
1258D ALA* 4.2 1.3 - - + +
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Residues in contact with LEU1051 (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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1042D THR* 3.6 31.9 - - + -
1047D LEU* 2.7 32.1 + - + +
1048D ASP* 3.7 7.6 - - - +
1049D ILE 3.2 0.2 - - - -
1050D ALA* 1.3 71.5 - - - +
1052D GLY* 1.3 55.3 + - - +
1053D ALA 2.9 10.0 + - - -
1055D GLY* 3.6 30.5 - - - +
1056D LEU* 4.0 7.4 - - + +
1221D VAL* 3.6 38.8 - - + -
1223D LEU* 4.3 9.0 - - + -
1246D VAL* 4.4 7.6 - - + -
1249D ASN* 3.2 22.2 + - - +
1251D ILE* 4.1 6.1 - - + +
1252D ALA* 3.3 3.6 - - - +
1253D ALA 5.2 0.2 - - - -
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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