Contacts of the helix formed by residues 159 - 171 (chain D) in PDB entry 3DH1
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 ARG 159 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 3.0 44.1 + - - +
30D MET* 4.1 24.6 - - + +
31D HIS* 6.2 2.2 - - - -
34D LYS* 5.1 8.1 - - - +
157D GLY 3.0 3.0 + - - -
158D TYR* 1.3 108.0 + - + +
160D ALA* 1.3 64.5 + - - +
161D GLU* 3.3 4.7 + - - +
162D GLU* 2.9 45.0 + - - +
163D ALA* 3.2 20.4 + - - +
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Residues in contact with ALA 160 (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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125D GLY 3.7 22.0 - - - +
126D CYS* 3.5 17.1 - - + +
157D GLY* 3.3 13.7 + - - +
158D TYR 3.3 1.6 - - - -
159D ARG* 1.3 75.9 - - - +
161D GLU* 1.3 55.9 + - + +
163D ALA* 3.3 0.8 + - - -
164D VAL* 2.8 38.7 + - - +
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Residues in contact with GLU 161 (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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159D ARG* 3.3 0.9 - - - -
160D ALA* 1.3 77.6 - - + +
162D GLU* 1.3 60.0 + - + +
164D VAL* 3.2 11.5 - - - +
165D GLU* 3.0 30.3 + - - +
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Residues in contact with GLU 162 (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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30D MET* 2.7 39.0 - - + +
159D ARG* 2.9 40.7 + - + +
161D GLU* 1.3 77.8 - - + +
163D ALA* 1.3 69.9 + - - +
165D GLU* 3.0 13.2 + - - +
166D MET* 3.0 24.9 + - + +
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Residues in contact with ALA 163 (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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30D MET* 4.1 5.6 - - - +
43D PRO* 5.3 0.3 - - - +
103D THR* 3.5 28.4 - - + +
125D GLY* 4.9 1.3 - - - -
126D CYS* 3.5 25.6 - - + +
159D ARG 3.2 11.2 + - - +
160D ALA 3.5 5.4 - - - +
162D GLU* 1.3 79.2 - - - +
164D VAL* 1.3 64.1 + - - +
166D MET* 3.0 16.8 + - - +
167D LEU* 3.0 21.0 + - - +
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Residues in contact with VAL 164 (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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126D CYS* 3.7 20.3 - - + -
127D GLN 5.2 3.6 - - - +
129D GLU* 5.7 4.9 - - - +
160D ALA 2.8 19.7 + - - +
161D GLU* 3.2 18.4 - - - +
163D ALA* 1.3 73.1 - - - +
165D GLU* 1.3 57.5 + - + +
167D LEU* 3.3 10.5 + - + +
168D LYS* 2.8 57.1 + - + +
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Residues in contact with GLU 165 (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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161D GLU 3.0 19.6 + - - +
162D GLU* 3.0 12.3 + - - +
164D VAL* 1.3 78.0 - - + +
166D MET* 1.3 57.5 + - + +
168D LYS* 3.3 8.9 + - + +
169D THR* 3.0 40.6 + - + +
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Residues in contact with MET 166 (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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30D MET* 3.5 44.0 - - + +
33D ALA* 3.9 20.9 - - + +
34D LYS* 4.1 38.1 - - - -
37D LEU* 4.1 13.3 - - + +
43D PRO* 3.7 16.8 - - + +
103D THR* 4.9 1.1 - - + -
162D GLU* 3.0 14.5 + - + +
163D ALA* 3.0 13.9 + - - +
165D GLU* 1.3 72.7 - - + +
167D LEU* 1.3 67.8 + - - +
169D THR* 3.2 8.8 + - - -
170D PHE* 2.9 24.9 + - - +
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Residues in contact with LEU 167 (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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42D VAL* 4.0 23.1 - - + -
43D PRO* 3.7 13.3 - - + +
44D VAL* 5.6 0.2 - - + -
104D VAL* 3.9 35.0 - - + -
126D CYS* 4.1 11.4 - - - -
127D GLN 4.6 6.1 - - - +
128D ASN* 5.6 2.9 - - - +
163D ALA 3.0 12.1 + - - +
164D VAL* 3.3 14.8 + - + +
166D MET* 1.3 76.3 - - - +
168D LYS* 1.3 62.5 + - + +
170D PHE* 3.4 3.0 + - + +
171D TYR* 3.0 66.8 + - + +
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Residues in contact with LYS 168 (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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129D GLU* 6.1 0.7 - - - -
164D VAL* 2.8 44.7 + - + +
165D GLU* 3.7 9.6 - - + +
167D LEU* 1.3 71.8 - - + +
169D THR* 1.3 67.7 + - + +
171D TYR* 3.3 18.6 + - + +
172D LYS* 3.4 25.8 + - - +
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Residues in contact with THR 169 (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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37D LEU* 4.5 12.7 - - - +
165D GLU* 3.0 25.4 + - + +
166D MET* 3.2 14.7 + - - -
168D LYS* 1.3 77.2 - - + +
170D PHE* 1.3 62.3 + - - +
172D LYS* 3.1 40.7 + - - +
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Residues in contact with PHE 170 (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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37D LEU* 3.9 14.7 - - + +
40D THR* 4.3 15.3 - - + -
41D GLU 3.8 22.7 - - - -
42D VAL* 3.4 31.9 - - + -
43D PRO* 3.6 21.1 - - + -
63D ASN* 5.3 5.2 - - - -
166D MET 2.9 17.4 + - - +
167D LEU* 3.5 4.9 - - + +
169D THR* 1.3 79.7 + - - +
171D TYR* 1.3 85.7 + + - +
172D LYS 3.0 12.9 + - - +
173D GLN* 4.1 11.1 + - + +
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Residues in contact with TYR 171 (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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42D VAL* 5.1 5.8 - - + +
128D ASN* 5.4 2.3 + - - -
130D ARG* 3.2 65.1 + - + +
167D LEU* 3.0 53.2 + - + +
168D LYS* 3.3 10.7 + - + +
170D PHE* 1.3 100.1 - + - +
172D LYS* 1.3 59.8 + - - +
173D GLN 3.7 6.7 + - - +
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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