Contacts of the helix formed by residues 1199 - 1208 (chain A) in PDB entry 4DDG
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 THR1199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191A GLU* 6.0 4.3 - - - -
1194A ILE* 4.0 2.6 - - - +
1197A GLY 4.8 3.8 - - - +
1198A ARG* 1.3 77.8 - - - +
1200A VAL* 1.3 68.5 + - - +
1201A LYS* 3.7 5.6 + - - +
1202A GLU* 3.2 41.7 + - - +
1203A PHE* 3.1 20.8 + - - +
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Residues in contact with VAL1200 (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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1183A LEU* 3.6 33.0 - - + +
1184A GLN* 4.2 5.2 - - + -
1187A SER* 3.4 35.0 - - - +
1190A PHE* 5.4 6.1 - - + -
1191A GLU* 5.2 12.5 - - + +
1194A ILE* 4.1 15.1 - - + +
1199A THR* 1.3 75.8 - - - +
1201A LYS* 1.3 62.1 + - + +
1203A PHE* 3.2 6.8 + - + +
1204A CYS* 2.9 29.9 + - - -
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Residues in contact with LYS1201 (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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1184A GLN* 3.4 33.0 - - + +
1199A THR* 3.4 5.0 + - - +
1200A VAL* 1.3 80.8 - - + +
1202A GLU* 1.3 61.5 + - + +
1204A CYS* 3.2 6.5 + - - +
1205A GLN* 2.9 52.7 + - + +
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Residues in contact with GLU1202 (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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1197A GLY 4.7 0.7 - - - +
1198A ARG* 3.4 14.5 - - + +
1199A THR* 3.2 44.1 + - - +
1200A VAL 3.3 0.4 - - - -
1201A LYS* 1.3 75.3 - - + +
1203A PHE* 1.3 59.2 + - - +
1205A GLN* 3.2 13.9 + - - +
1206A GLN* 2.9 50.4 + - - +
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Residues in contact with PHE1203 (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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1183A LEU* 4.2 16.6 - - + -
1194A ILE* 4.0 32.5 - - + -
1195A GLU* 4.0 11.4 - - - -
1198A ARG* 3.5 38.7 - - - +
1199A THR 3.1 13.8 + - - +
1200A VAL* 3.2 11.9 + - + +
1202A GLU* 1.3 76.4 - - - +
1204A CYS* 1.3 59.2 + - - +
1206A GLN* 4.7 1.3 - - - -
1207A GLU* 2.9 37.7 + - + -
1208A VAL* 3.5 21.5 - - + +
1216A ASP* 5.8 0.7 - - + -
1218A ILE* 3.9 20.4 - - + -
1219A HIS* 3.7 25.6 - + - -
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Residues in contact with CYS1204 (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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1180A SER* 3.2 33.7 - - - +
1183A LEU* 3.6 38.4 - - - -
1184A GLN* 3.8 16.2 - - - +
1200A VAL* 2.9 17.6 + - - +
1201A LYS 3.5 8.1 - - - +
1202A GLU 3.2 0.2 - - - -
1203A PHE* 1.3 77.4 - - - +
1205A GLN* 1.3 60.3 + - + +
1206A GLN 3.2 1.0 + - - -
1208A VAL* 3.3 10.0 + - - -
1209A GLU* 2.8 32.5 + - - +
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Residues in contact with GLN1205 (chain A).
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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1201A LYS* 2.9 49.5 + - + +
1202A GLU* 3.2 14.3 + - - +
1204A CYS* 1.3 75.7 - - - +
1206A GLN* 1.3 59.2 + - - +
1209A GLU* 4.5 17.4 - - - +
1210A PRO* 3.2 18.4 - - - +
92B GLN* 3.8 38.0 - - + +
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Residues in contact with GLN1206 (chain A).
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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1198A ARG* 3.0 43.5 + - - +
1202A GLU* 2.9 32.0 + - - +
1203A PHE 4.2 0.2 - - - +
1205A GLN* 1.3 78.3 - - - +
1207A GLU* 1.3 64.4 + - - +
1208A VAL 3.5 1.1 - - - -
1210A PRO* 3.1 20.7 - - - +
1213A LYS* 3.5 18.2 + - - +
91B SER 5.2 0.6 - - - +
92B GLN* 3.9 36.3 + - + +
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Residues in contact with GLU1207 (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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1176A ARG* 4.4 1.0 + - - -
1195A GLU* 5.3 0.9 - - - +
1198A ARG* 3.5 27.3 + - - +
1203A PHE* 2.9 40.1 + - + +
1206A GLN* 1.3 80.5 - - - +
1208A VAL* 1.3 60.4 + - - +
1213A LYS* 3.9 30.8 + - + +
1214A GLU* 3.5 21.9 - - + +
1219A HIS* 2.9 20.2 + - + +
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Residues in contact with VAL1208 (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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1093A TYR* 4.4 1.8 - - - +
1176A ARG* 3.1 52.8 + - - +
1179A THR* 4.1 9.4 - - + -
1180A SER* 3.7 20.4 - - - +
1183A LEU* 4.1 8.3 - - + -
1203A PHE* 3.5 16.6 - - + +
1204A CYS* 3.3 25.9 + - - -
1206A GLN 3.5 1.2 - - - -
1207A GLU* 1.3 80.9 - - - +
1209A GLU* 1.3 67.8 + - - +
1210A PRO* 3.3 3.6 - - - +
1219A HIS* 3.5 21.5 - - + +
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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