Contacts of the helix formed by residues 1164 - 1171 (chain A) in PDB entry 3DKF
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 ASP1164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SX8 3.1 34.3 + - + -
1162A HIS 4.0 0.5 - - - +
1163A GLY* 1.3 74.2 - - - -
1165A LEU* 1.3 64.1 + - - +
1166A ARG* 3.2 12.6 + - - +
1167A ASN* 2.9 47.7 + - - +
1168A PHE* 3.1 22.3 + - - +
1208A ARG* 3.6 24.2 - - - +
1210A CYS 3.3 7.4 - - - +
1211A MET* 4.0 5.7 - - + +
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Residues in contact with LEU1165 (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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1163A GLY 3.9 0.6 + - - -
1164A ASP* 1.3 72.5 - - - +
1166A ARG* 1.3 63.2 + - - +
1168A PHE* 3.5 3.9 + - + +
1169A ILE* 3.2 28.7 + - + +
1184A PHE* 3.9 32.5 - - + -
1188A VAL* 4.3 11.2 - - + -
1207A ALA* 3.3 20.6 + - + +
1210A CYS* 2.7 33.6 + - + +
1211A MET* 4.3 2.9 - - - +
1212A LEU* 4.3 19.7 - - + -
1218A VAL* 4.1 14.4 - - + -
1272A LEU* 4.8 2.5 - - + -
1276A LEU* 3.9 23.6 - - + -
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Residues in contact with ARG1166 (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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1164A ASP* 3.2 10.1 + - - +
1165A LEU* 1.3 76.5 - - - +
1167A ASN* 1.3 72.2 + - - +
1169A ILE* 3.3 8.0 - - - +
1170A ARG* 3.1 57.0 + - - +
1207A ALA* 3.4 9.4 + - + -
1208A ARG* 3.7 29.8 - - + +
1249A TRP* 5.9 2.2 - - - -
1275A GLU* 4.1 18.4 + - - +
1280A GLY* 3.0 32.7 + - - -
1281A ALA 4.2 1.2 + - - -
1282A PRO* 3.9 12.9 - - - +
1359A VAL 5.1 2.0 + - - -
1361A GLU* 3.9 26.9 - - - +
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Residues in contact with ASN1167 (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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1A SX8 3.8 12.7 - - - -
1164A ASP* 2.9 35.8 + - - +
1166A ARG* 1.3 82.4 + - - +
1168A PHE* 1.3 63.3 + - - +
1170A ARG* 3.4 17.5 + - - +
1171A ASN* 3.2 22.7 + - - +
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Residues in contact with PHE1168 (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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1162A HIS* 3.7 49.2 + + + +
1164A ASP 3.1 17.5 + - - +
1165A LEU* 3.7 9.4 - - + +
1167A ASN* 1.3 79.1 - - - +
1169A ILE* 1.3 73.0 + - + +
1171A ASN* 3.3 4.0 + - - -
1174A HIS* 2.8 65.3 + + + +
1176A PRO* 6.4 2.0 - - + -
1184A PHE* 4.0 17.3 - + - -
1212A LEU* 3.5 20.6 - - + -
1216A PHE* 3.7 22.0 - + - -
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Residues in contact with ILE1169 (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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1165A LEU* 3.2 24.6 + - + +
1166A ARG* 3.3 18.6 - - - +
1168A PHE* 1.3 87.8 - - + +
1170A ARG* 1.3 59.9 + - - +
1174A HIS* 5.8 0.7 - - - -
1176A PRO* 5.7 4.7 - - + -
1181A LEU* 3.6 25.1 - - + -
1184A PHE* 4.3 4.0 - - + -
1207A ALA* 4.9 5.2 - - + -
1275A GLU 3.5 26.5 - - - +
1276A LEU* 3.8 19.7 - - + +
1279A ARG* 3.0 48.3 + - + +
1280A GLY* 3.5 8.1 - - - +
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Residues in contact with ARG1170 (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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1166A ARG* 3.1 56.5 + - - +
1167A ASN* 3.8 15.0 + - - +
1168A PHE 3.3 0.2 - - - -
1169A ILE* 1.3 75.8 - - - +
1171A ASN* 1.3 64.5 + - - +
1172A GLU* 3.1 6.4 + - - +
1279A ARG* 3.3 22.4 + - - +
1280A GLY* 3.0 28.5 + - - -
1281A ALA* 4.6 0.8 - - - +
1282A PRO* 4.7 6.9 - - - +
1352A VAL* 5.4 4.9 - - - +
1356A TYR 5.3 4.0 + - - -
1358A ASN* 5.2 12.1 - - - +
1359A VAL 4.9 8.7 + - - -
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Residues in contact with ASN1171 (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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1167A ASN 3.2 12.9 + - - +
1168A PHE 3.5 3.6 - - - +
1169A ILE 3.2 1.0 - - - -
1170A ARG* 1.3 72.9 - - - +
1172A GLU* 1.3 59.9 + - - +
1173A THR* 2.5 47.9 + - - +
1174A HIS* 3.0 45.9 + - + +
1279A ARG* 2.9 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