Contacts of the helix formed by residues 1220 - 1229 (chain A) in PDB entry 2PDA
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 SER1220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193A GLU* 6.1 0.2 - - - +
1194A PHE* 4.0 12.5 - - - -
1219A THR* 1.3 70.9 - - - +
1221A GLU* 1.3 64.5 + - - +
1223A GLN* 2.7 35.3 + - - +
1224A GLY 2.9 10.7 + - - -
1077B ARG 4.7 1.4 + - - -
1078B LYS* 3.1 28.1 + - - +
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Residues in contact with GLU1221 (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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1219A THR* 3.2 19.9 - - + +
1220A SER* 1.3 82.6 - - - +
1222A GLN* 1.3 57.3 + - + +
1224A GLY* 4.4 2.7 - - - +
1225A ASP* 2.8 33.1 + - + +
1078B LYS* 2.9 42.1 + - - +
1082B LYS* 3.1 23.5 + - - +
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Residues in contact with GLN1222 (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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1217A ALA 5.3 1.3 - - - +
1218A GLY* 4.7 2.0 - - - -
1219A THR* 3.0 39.5 + - + +
1221A GLU* 1.3 76.6 - - + +
1223A GLN* 1.3 66.2 + - - +
1225A ASP* 3.5 10.9 - - - +
1226A LEU* 3.1 24.3 + - - +
1229A ARG* 4.7 0.5 + - - -
680B ASN* 5.9 0.7 - - - -
749B GLY* 2.9 33.8 + - - +
752B ALA* 3.6 8.6 - - + +
753B ASP* 3.1 28.1 + - - +
764B MET* 3.6 32.2 - - + +
1082B LYS* 5.4 0.2 - - - +
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Residues in contact with GLN1223 (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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1194A PHE* 3.8 6.9 - - - -
1213A ASP* 2.9 28.6 + - - +
1217A ALA* 3.6 29.0 + - + +
1218A GLY 2.7 28.0 + - - -
1219A THR 2.7 12.3 + - - -
1220A SER* 2.7 13.0 + - - +
1222A GLN* 1.3 77.9 - - - +
1224A GLY* 1.3 53.5 + - - +
1226A LEU* 3.2 8.7 - - - +
1227A SER* 3.0 25.5 + - - -
680B ASN* 4.6 4.5 - - - +
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Residues in contact with GLY1224 (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 SER 2.9 11.6 + - - -
1221A GLU* 3.9 3.1 - - - -
1223A GLN* 1.3 73.4 - - - +
1225A ASP* 1.3 57.2 + - - +
1226A LEU 2.8 1.3 - - - -
1227A SER* 2.9 8.3 + - - -
1228A LYS* 2.7 38.6 + - - +
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Residues in contact with ASP1225 (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 GLU 2.8 20.3 + - - +
1222A GLN* 3.5 14.4 - - - +
1224A GLY* 1.3 71.0 - - - +
1226A LEU* 1.3 58.0 + - - +
1228A LYS* 3.3 13.9 - - - +
1229A ARG* 2.7 70.4 + - - +
763B VAL* 4.8 5.6 - - - +
764B MET* 5.6 0.9 + - - +
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Residues in contact with LEU1226 (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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1222A GLN 3.1 20.1 + - - +
1223A GLN* 3.2 5.8 - - - +
1224A GLY 2.8 0.6 - - - -
1225A ASP* 1.3 75.3 + - - +
1227A SER* 1.3 60.6 + - - +
1228A LYS 3.1 1.3 - - - -
1229A ARG* 3.0 54.4 + - - +
1230A THR* 3.4 21.0 + - + +
680B ASN* 3.6 35.0 - - + +
764B MET* 3.6 13.2 - - + +
765B GLN* 4.6 2.5 - - - +
766B PRO* 3.9 20.2 - - + -
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Residues in contact with SER1227 (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 GLN 3.0 13.2 + - - -
1224A GLY* 2.9 11.3 + - - -
1226A LEU* 1.3 70.5 - - - +
1228A LYS* 1.3 57.8 + - - +
1229A ARG 2.9 10.2 + - - -
1230A THR* 4.1 5.6 - - - -
1231A LYS* 3.3 28.4 + - - +
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Residues in contact with LYS1228 (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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1224A GLY 2.7 17.4 + - - +
1225A ASP* 3.3 8.7 - - - +
1227A SER* 1.3 75.7 - - - +
1229A ARG* 1.3 65.4 + - - +
1231A LYS* 4.4 20.6 - - + -
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Residues in contact with ARG1229 (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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1222A GLN 4.7 0.2 + - - -
1225A ASP* 2.7 55.0 + - - +
1226A LEU* 3.2 32.8 - - - +
1227A SER 2.9 0.8 - - - -
1228A LYS* 1.3 82.8 - - + +
1230A THR* 1.3 69.6 + - + +
1231A LYS* 4.9 7.0 - - - +
763B VAL* 3.5 14.5 - - - +
764B MET* 3.2 22.0 + - - +
765B GLN* 3.1 24.9 + - - +
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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