Contacts of the helix formed by residues 1218 - 1228 (chain A) in PDB entry 5M64
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 GLY1218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1200A MET* 4.6 5.8 - - - -
1202A LEU 4.4 3.8 - - - -
1217A LEU* 1.3 74.6 - - - +
1219A ILE* 1.3 64.2 + - - -
1220A PRO* 4.4 0.2 - - - -
1221A ARG* 3.1 1.9 + - - +
1222A LEU* 2.9 30.3 + - - +
1569A VAL* 4.2 15.9 - - - +
1573A TYR* 3.6 26.7 + - - -
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Residues in contact with ILE1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015A ARG* 3.7 31.2 - - + -
1016A SER* 6.4 0.2 - - - -
1197A SER* 4.1 9.6 - - - +
1200A MET* 3.7 32.7 + - + -
1201A THR* 3.6 39.7 - - + -
1202A LEU 4.9 2.7 + - - +
1218A GLY* 1.3 71.2 - - - -
1220A PRO* 1.3 72.6 - - + +
1222A LEU* 4.5 3.6 - - + +
1223A ARG* 2.9 42.7 + - + +
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Residues in contact with PRO1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A LEU 5.4 2.9 - - - +
1203A ASN* 5.3 10.3 - - - +
1216A THR* 5.2 12.4 + - + -
1217A LEU 3.6 11.9 - - - +
1218A GLY 3.6 2.9 - - - -
1219A ILE* 1.3 94.5 - - + +
1221A ARG* 1.3 54.6 - - - +
1223A ARG* 4.6 17.9 + - - +
1224A GLU* 3.0 25.2 + - - +
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Residues in contact with ARG1221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215A VAL* 6.3 0.4 - - - -
1216A THR* 3.2 42.8 + - - +
1217A LEU* 4.1 7.3 + - - -
1218A GLY 3.1 8.1 + - - +
1219A ILE 3.1 0.8 - - - -
1220A PRO* 1.3 78.6 - - - +
1222A LEU* 1.3 65.5 + - - +
1223A ARG 3.4 0.2 - - - -
1224A GLU* 3.2 7.1 + - - +
1225A ILE* 3.1 54.1 + - - +
1233A ILE* 4.6 16.0 - - - +
1544A ASN* 2.5 49.5 + - - +
1565A GLU* 2.6 35.3 + - - +
1569A VAL* 3.8 16.2 - - + +
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Residues in contact with LEU1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019A LEU* 4.1 28.9 - - + -
1193A VAL* 5.0 10.3 - - + +
1197A SER* 5.8 0.2 - - - +
1200A MET* 3.7 30.1 - - + -
1218A GLY 2.9 15.5 + - - +
1219A ILE* 4.2 3.6 - - + +
1221A ARG* 1.3 77.8 - - - +
1223A ARG* 1.3 64.4 + - + +
1225A ILE* 3.4 1.6 + - - +
1226A VAL* 3.1 42.3 + - + +
1566A ILE* 3.7 28.9 - - + -
1569A VAL* 5.0 8.5 - - + +
1570A PHE* 4.1 19.3 - - + -
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Residues in contact with ARG1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015A ARG* 5.1 20.5 - - - +
1018A TYR* 5.2 7.2 - - + -
1019A LEU* 6.0 0.4 - - + -
1219A ILE* 2.9 30.0 + - + +
1220A PRO* 4.6 17.2 + - - +
1222A LEU* 1.3 81.9 - - + +
1224A GLU* 1.3 71.7 + - - +
1227A MET* 3.4 41.2 + - + +
1228A THR* 3.2 33.2 - - - +
55S T 4.2 16.2 + - - -
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Residues in contact with GLU1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220A PRO 3.0 24.0 + - - +
1221A ARG* 3.2 8.0 + - - +
1222A LEU 3.1 0.8 - - - -
1223A ARG* 1.3 90.0 + - - +
1225A ILE* 1.3 71.1 + - + +
1228A THR* 2.3 58.7 + - - +
1230A SER* 3.3 15.8 + - - +
1231A ALA 5.1 1.9 + - - -
1233A ILE* 3.5 33.9 - - + +
55S T 4.6 7.2 + - - -
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Residues in contact with ILE1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221A ARG* 3.1 56.7 + - - +
1222A LEU* 4.3 2.5 - - - +
1224A GLU* 1.3 81.7 - - + +
1226A VAL* 1.3 66.1 + - + +
1227A MET 3.8 0.2 + - - -
1230A SER* 3.2 28.6 + - - +
1233A ILE* 5.8 2.0 - - + -
1544A ASN 5.3 0.2 - - - +
1545A ASP* 6.2 0.9 - - - -
1546A VAL* 4.4 20.9 - - + -
1562A ILE* 5.5 7.4 - - + -
1565A GLU* 3.8 21.1 - - - +
1566A ILE* 5.1 6.1 - - + -
1589A MET* 3.5 20.0 - - + +
1595A TYR* 3.9 1.2 + - - -
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Residues in contact with VAL1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019A LEU* 4.6 4.7 - - + -
1023A LEU* 3.9 14.6 - - + -
1193A VAL* 5.9 4.0 - - + -
1222A LEU* 3.1 43.7 + - + +
1223A ARG* 4.7 1.6 - - - +
1224A GLU 3.4 0.2 - - - -
1225A ILE* 1.3 84.2 - - + +
1227A MET* 1.3 73.0 + - + +
1229A ALA 5.4 0.2 - - - -
1566A ILE* 5.1 5.4 - - + -
1585A ILE* 5.6 8.7 - - + -
1589A MET* 4.4 6.0 - - - +
1597A ALA* 3.4 5.6 - - - +
1598A PHE* 3.3 43.1 - - + +
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Residues in contact with MET1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018A TYR* 3.5 40.2 - - + +
1019A LEU* 3.8 22.7 - - + +
1022A CYS* 3.6 22.4 - - - -
1023A LEU* 3.7 14.4 - - + -
1223A ARG* 3.4 32.7 + - + +
1226A VAL* 1.3 91.4 - - + +
1228A THR* 1.3 59.1 + - + +
1229A ALA 3.1 6.5 + - - -
1597A ALA 3.0 17.5 - - - +
1598A PHE* 4.1 13.5 - - + +
1599A ASN* 3.1 19.3 + - + +
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Residues in contact with THR1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223A ARG* 3.2 48.7 - - - +
1224A GLU* 2.3 53.7 + - - +
1227A MET* 1.3 76.0 - - + +
1229A ALA* 1.3 63.8 + - - +
1230A SER* 4.4 1.0 + - - -
1599A ASN* 4.9 0.9 - - - -
55S T 4.0 16.2 - - - +
56S A 3.0 18.6 + - - -
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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