Contacts of the helix formed by residues 160 - 169 (chain C) in PDB entry 1DGH
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 LEU 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 5.0 1.1 - - - +
39A LEU* 3.3 51.8 - - + +
405B TYR 3.8 13.9 - - - +
406B PRO* 4.1 4.9 - - + -
155C ILE* 3.7 15.0 - - + -
157C ASP* 3.3 24.8 + - + +
158C PRO 3.0 1.2 - - - -
159C ILE* 1.3 79.3 - - + +
161C PHE* 1.3 59.9 + - - +
162C PRO* 3.4 1.6 - - - -
163C SER* 3.3 8.9 + - - -
164C PHE* 2.9 27.4 + - - +
185C PHE* 4.1 9.5 - - + -
189C ARG* 3.9 33.7 - - - +
191C GLU* 5.0 3.4 - - - +
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Residues in contact with PHE 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.8 18.2 - + - -
74C VAL* 4.5 8.3 - - + -
75C HIS* 6.1 1.6 - - - -
153C PHE* 3.7 33.7 - + - -
155C ILE* 3.4 14.4 - - + +
158C PRO 3.0 16.2 + - - +
160C LEU* 1.3 75.4 - - - +
162C PRO* 1.3 69.7 - - + +
164C PHE* 3.2 3.1 + + - +
165C ILE* 2.9 51.7 + - + +
2002C HEM 3.3 79.4 - + + -
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Residues in contact with PRO 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 4.3 27.4 - - + +
61A MET* 3.8 19.7 - - + -
64A PHE* 3.9 39.9 - - + -
386B TYR 5.8 0.7 - - - +
158C PRO 3.6 8.1 - - - +
159C ILE* 3.8 8.5 - - - +
160C LEU 3.7 2.5 - - - -
161C PHE* 1.3 92.6 - - + +
163C SER* 1.3 56.7 + - - +
165C ILE* 3.3 1.0 + - - +
166C HIS* 2.8 43.7 + - + -
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Residues in contact with SER 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 4.4 11.1 + - - -
60A GLU* 4.5 3.8 + - - -
386B TYR* 4.7 4.4 - - - +
403B ASN 4.6 1.4 + - - -
404B TYR* 3.4 16.2 - - - +
405B TYR* 3.0 49.0 + - - +
159C ILE 5.2 0.2 + - - -
160C LEU* 3.3 10.2 + - - -
161C PHE 3.2 0.6 - - - -
162C PRO* 1.3 76.8 - - - +
164C PHE* 1.3 65.8 + - - +
166C HIS* 3.2 5.3 + - - +
167C SER* 2.9 20.3 + - - -
185C PHE* 4.0 4.5 - - - -
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Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL* 6.0 2.9 - - + -
153C PHE* 3.9 22.7 - + - -
154C PHE* 3.3 43.7 - + + -
155C ILE* 4.4 5.8 - - + -
160C LEU 2.9 17.0 + - - +
161C PHE* 3.6 8.3 - + - +
163C SER* 1.3 75.1 - - - +
165C ILE* 1.3 83.0 + - + +
167C SER* 2.7 23.5 + - - -
168C GLN* 3.1 36.9 + - + +
185C PHE* 3.6 32.7 - + + -
186C TRP* 3.4 22.7 - + - -
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.9 16.6 - - + -
74C VAL* 3.3 31.9 - - + -
116C VAL* 4.4 15.3 - - + -
153C PHE* 5.4 1.1 - - + -
161C PHE* 2.9 50.4 + - + +
162C PRO 3.8 2.9 - - - +
164C PHE* 1.3 95.8 - - + +
166C HIS* 1.3 65.9 + - + +
168C GLN* 3.1 9.0 + - + +
169C LYS* 3.0 39.6 + - + +
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Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.2 8.8 - + - -
67A GLU* 2.6 37.9 + - - -
386B TYR* 3.0 25.0 + - + +
387B GLN* 5.0 0.2 - - - -
388B ARG* 4.5 12.5 - - + +
403B ASN* 2.7 46.2 + - + +
162C PRO* 2.8 32.6 + - + +
163C SER* 3.4 5.8 - - - +
165C ILE* 1.3 78.6 - - + +
167C SER* 1.3 62.6 + - - +
169C LYS* 3.0 21.2 + - + +
170C ARG 4.5 0.9 + - - +
181C MET* 3.2 14.9 - - - +
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B TYR* 4.1 10.0 - - - +
163C SER 2.9 12.2 + - - -
164C PHE* 2.7 27.0 + - - -
166C HIS* 1.3 76.4 - - - +
168C GLN* 1.3 61.2 + - - +
169C LYS 3.3 2.5 - - - +
178C ASP 4.3 0.3 - - - +
181C MET* 3.4 39.0 - - - +
182C VAL* 3.4 27.6 + - - +
185C PHE* 3.7 19.3 - - - +
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Residues in contact with GLN 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL* 6.3 2.8 - - + +
117C ALA* 3.8 24.2 - - + +
128C ASP* 4.4 14.5 + - - -
129C PRO* 6.0 1.4 - - - +
154C PHE* 5.7 1.6 - - - -
164C PHE* 3.1 46.0 + - + +
165C ILE* 3.1 13.6 + - + +
167C SER* 1.3 77.0 + - - +
169C LYS* 1.3 64.7 - - + +
177C LYS* 4.1 9.4 - - - +
182C VAL* 3.7 23.4 - - - +
186C TRP* 3.2 31.9 - - - -
199C LEU* 5.5 4.0 - - - +
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ARG* 3.2 31.8 - - - +
71C GLU* 5.1 3.2 + - - -
72C ARG 5.6 0.2 + - - -
73C VAL 3.2 17.0 + - - -
74C VAL* 4.0 6.4 - - - +
76C ALA* 6.0 1.4 - - - +
116C VAL 4.3 2.4 + - - -
117C ALA* 2.7 41.2 + - + +
118C GLY 4.8 3.0 + - - -
119C GLU* 4.7 12.8 + - - +
165C ILE* 3.0 34.7 + - + +
166C HIS* 3.0 13.7 + - + +
167C SER 4.2 2.9 - - - +
168C GLN* 1.3 84.9 - - + +
170C ARG* 1.3 71.7 + - + +
171C ASN 4.1 0.3 + - - -
177C LYS* 3.7 21.3 - - - +
178C ASP 4.2 5.2 + - - -
181C MET* 4.6 1.7 - - - +
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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