Contacts of the helix formed by residues 163 - 175 (chain D) in PDB entry 1DE4
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 163 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159D ALA* 2.8 40.0 + - - +
162D GLU* 1.3 75.3 - - + +
164D ASP* 1.3 97.7 + - - +
166D PRO* 3.3 9.8 - - - +
167D ALA* 3.4 14.5 + - + +
651F ARG* 5.9 4.4 - - - +
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Residues in contact with ASP 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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160D TYR* 3.2 37.4 + - + +
163D ARG* 1.3 105.9 + - - +
165D CYS* 1.3 68.2 + - - +
167D ALA* 2.9 19.3 + - - +
168D GLN* 2.9 14.7 + - - +
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Residues in contact with CYS 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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8D LEU* 3.8 13.0 - - - +
101D GLY* 3.7 11.0 - - - -
102D CYS* 2.0 52.7 - - + -
160D TYR* 2.8 49.3 + - + +
161D LEU* 3.9 5.8 - - - +
164D ASP* 1.3 70.7 - - - +
166D PRO* 1.3 70.6 - - + +
168D GLN* 3.0 7.1 + - - +
169D LEU* 2.9 21.5 + - - +
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Residues in contact with PRO 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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102D CYS* 3.5 6.5 - - - -
104D MET* 3.5 22.1 - - + +
110D THR* 3.8 24.7 - - + +
161D LEU 3.0 25.8 - - - +
162D GLU 3.4 13.9 - - - +
163D ARG 3.3 13.7 - - - +
165D CYS* 1.3 87.9 - - + +
167D ALA* 1.3 62.2 + - - +
169D LEU* 3.1 5.3 + - + +
170D GLN* 3.1 25.7 + - - +
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Residues in contact with ALA 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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163D ARG* 3.4 12.2 + - + +
164D ASP* 2.9 13.5 + - - +
166D PRO* 1.3 79.3 - - - +
168D GLN* 1.3 60.3 + - - +
170D GLN* 3.2 19.7 + - - +
171D GLN* 3.2 23.7 + - - +
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Residues in contact with GLN 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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8D LEU* 3.5 13.3 - - - +
10D TYR* 2.8 31.7 + - - -
36D PHE* 5.2 0.2 - - - -
61D MET* 5.6 2.5 - - + +
64D GLN* 6.5 0.7 - - - -
65D LEU* 3.3 21.8 + - - +
68D SER* 5.9 2.6 + - - -
72D TRP* 5.5 1.6 - - - -
160D TYR* 4.0 13.7 + - - -
164D ASP 2.9 11.9 + - - +
165D CYS* 3.7 5.3 - - - +
167D ALA* 1.3 74.3 - - - +
169D LEU* 1.3 64.5 + - - +
171D GLN* 3.5 20.7 + - + +
172D LEU* 3.1 32.6 + - + +
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Residues in contact with LEU 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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6D HIS* 4.1 16.6 - - + +
7D SER* 3.8 19.7 - - - +
8D LEU* 3.7 28.7 - - + +
31D VAL* 4.1 16.2 - - + -
102D CYS* 4.6 7.2 - - - +
104D MET* 3.8 37.7 - - + +
165D CYS 2.9 12.1 + - - +
166D PRO* 3.1 9.6 + - + +
168D GLN* 1.3 73.5 - - - +
170D GLN* 1.3 66.4 + - - +
172D LEU* 3.2 3.7 + - + +
173D LEU* 2.9 42.1 + - + +
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Residues in contact with GLN 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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104D MET* 3.8 23.3 - - + +
108D ASN* 4.1 20.0 - - - +
166D PRO 3.1 19.7 + - - +
167D ALA* 3.2 12.5 + - - +
169D LEU* 1.3 75.4 - - - +
171D GLN* 1.3 66.2 + - + +
173D LEU* 2.9 24.9 + - - +
174D GLU* 3.1 27.8 + - - +
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Residues in contact with GLN 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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60D GLN* 5.1 5.2 + - - -
61D MET* 3.3 39.9 - - - +
167D ALA* 3.2 13.8 + - - +
168D GLN* 3.5 32.8 - - + +
170D GLN* 1.3 79.9 - - + +
172D LEU* 1.3 59.6 + - + +
174D GLU* 3.7 9.4 + - - +
175D LEU* 3.1 29.1 + - - +
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Residues in contact with LEU 172 (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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8D LEU* 3.8 18.8 - - + -
31D VAL* 4.3 15.3 - - + -
36D PHE* 3.6 40.2 - - + -
52D TRP* 3.2 31.2 - - + -
57D ILE* 4.4 21.5 - - + -
61D MET* 5.5 4.7 - - - -
168D GLN* 3.1 24.9 + - + +
169D LEU* 3.5 8.7 - - - +
170D GLN 3.1 0.6 - - - -
171D GLN* 1.3 77.7 - - + +
173D LEU* 1.3 61.9 + - - +
175D LEU* 3.6 8.0 + - + -
176D GLY* 3.1 19.4 + - - -
180D LEU* 4.5 0.5 - - - +
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Residues in contact with LEU 173 (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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6D HIS* 3.4 40.4 - - + +
31D VAL* 4.1 8.3 - - + -
32D ASP* 3.4 25.4 - - - +
104D MET* 5.4 2.7 - - - -
169D LEU* 2.9 27.1 + - + +
170D GLN* 2.9 23.2 + - - +
172D LEU* 1.3 72.8 - - - +
174D GLU* 1.3 58.7 + - + +
175D LEU 3.0 1.3 - - - -
176D GLY* 2.6 22.9 + - - -
177D ARG* 2.9 14.1 + - - +
180D LEU* 4.0 13.1 - - + +
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Residues in contact with GLU 174 (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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170D GLN* 3.1 26.3 + - - +
171D GLN* 4.1 6.4 + - - +
173D LEU* 1.3 79.2 - - + +
175D LEU* 1.3 61.4 + - - +
176D GLY 3.1 1.0 + - - -
177D ARG* 3.6 17.7 + - - +
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Residues in contact with LEU 175 (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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52D TRP* 3.2 11.1 - - + -
56D ARG* 2.8 61.2 - - + +
57D ILE* 3.3 41.1 - - + -
58D SER* 6.0 0.2 - - - -
61D MET* 3.5 28.7 - - + -
171D GLN 3.1 15.8 + - - +
172D LEU* 3.6 10.3 - - + +
173D LEU 3.0 0.2 - - - -
174D GLU* 1.3 78.7 - - - +
176D GLY* 1.3 56.6 + - - +
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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