Contacts of the helix formed by residues 158 - 167 (chain M) in PDB entry 1H2I
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 PHE 158 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76L ASN* 3.5 14.4 + - - +
81L TYR* 3.9 23.2 - + + +
43M LEU* 3.3 30.3 - - + +
79M PHE* 4.1 19.3 - + + -
113M VAL* 4.1 15.9 - - + -
115M LEU* 3.3 46.0 - - + -
119M SER* 4.6 4.3 - - - -
120M TYR* 4.7 13.0 - - - -
121M HIS* 3.6 28.7 - + - -
154M ALA 4.6 0.4 - - - -
155M LEU* 2.9 42.3 + - + +
157M SER* 1.3 80.8 - - - +
159M GLY* 1.3 55.7 + - - +
162M LEU* 4.8 3.8 - - + -
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Residues in contact with GLY 159 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L ASN* 4.3 4.3 - - - -
76L ASN* 3.9 9.9 - - - -
43M LEU* 4.0 8.5 - - - -
155M LEU 4.3 0.2 + - - -
156M ARG 3.0 8.1 + - - +
157M SER 3.2 1.4 - - - -
158M PHE* 1.3 81.6 - - - +
160M ASN* 1.3 68.8 + - - -
161M ALA 3.3 2.5 - - - -
162M LEU* 3.1 10.7 + - - +
163M GLY 3.4 0.5 + - - -
164M ASN* 3.0 24.7 + - - +
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Residues in contact with ASN 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L HIS* 6.0 0.2 - - - -
73L ASN* 3.2 33.2 + - - +
43M LEU 3.0 4.2 + - - -
44M ARG* 2.9 25.5 + - - +
45M GLN 3.2 17.3 - - - +
46M ARG* 4.2 22.0 + - - +
47M LEU* 3.0 12.0 - - - +
159M GLY* 1.3 71.8 - - - -
161M ALA* 1.3 56.3 + - - +
163M GLY 2.7 23.6 + - - -
164M ASN* 3.4 10.4 + - - +
165M CYS* 3.6 23.0 + - + +
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Residues in contact with ALA 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L LYS* 4.4 12.1 - - + -
42M ALA 3.3 26.5 - - - +
43M LEU* 2.8 19.5 + - - +
45M GLN 3.0 11.2 + - - +
47M LEU* 3.7 10.1 - - - +
74M LEU* 3.6 25.1 - - - +
78M MET* 3.7 17.0 - - + -
159M GLY 3.3 0.2 - - - -
160M ASN* 1.3 70.9 - - - +
162M LEU* 1.3 63.2 + - + +
163M GLY 3.4 0.2 - - - -
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Residues in contact with LEU 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M LEU* 3.6 24.2 - - + +
66M ILE* 5.2 1.1 - - - -
71M VAL* 4.2 16.6 - - + +
74M LEU* 4.0 16.4 - - + +
75M ALA* 3.9 28.3 - - + +
78M MET* 4.1 21.3 - - + -
79M PHE* 4.6 9.2 - - + -
152M LYS 4.8 0.7 - - - +
155M LEU* 3.6 40.8 - - + +
156M ARG* 3.8 14.2 + - - +
158M PHE* 4.8 5.2 - - + -
159M GLY 3.1 8.9 + - - +
160M ASN 2.9 1.4 + - - -
161M ALA* 1.3 85.1 - - + +
163M GLY* 1.3 57.1 + - - +
164M ASN 3.8 0.2 - - - -
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Residues in contact with GLY 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M LEU* 4.3 3.0 - - - +
66M ILE* 3.9 22.9 - - - -
156M ARG* 3.6 16.0 - - - -
160M ASN 2.7 14.9 + - - -
161M ALA 3.4 1.4 + - - -
162M LEU* 1.3 74.5 - - - +
164M ASN* 1.3 63.3 + - - +
165M CYS* 3.0 4.6 + - - -
166M ILE* 3.2 25.3 + - - +
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Residues in contact with ASN 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L HIS* 3.0 49.7 - - - +
72L ILE* 3.5 26.9 - - - +
73L ASN* 3.3 19.4 + - - +
156M ARG* 3.3 19.6 + - - +
159M GLY 3.0 25.8 + - - +
160M ASN* 3.4 4.6 + - - +
162M LEU 3.8 0.6 - - - -
163M GLY* 1.3 75.8 - - - +
165M CYS* 1.3 61.9 + - - +
166M ILE 3.4 0.2 - - - -
167M LEU* 3.2 15.3 - - - +
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Residues in contact with CYS 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L HIS* 5.7 0.4 - - - -
46M ARG* 4.0 25.1 - - - +
47M LEU* 3.2 40.4 - - - -
66M ILE* 5.7 0.2 - - - -
160M ASN* 3.6 19.5 + - + +
163M GLY* 3.1 3.4 - - - -
164M ASN* 1.3 76.9 - - - +
166M ILE* 1.3 62.4 + - - +
167M LEU 2.6 19.2 + - - -
168M ASP* 2.6 27.3 + - - +
171M TYR* 3.6 30.9 - - + -
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Residues in contact with ILE 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M ILE* 4.3 11.9 - - + -
64M CYS* 3.4 43.1 - - + +
65M TYR* 3.7 7.9 - - - +
66M ILE* 3.8 27.6 - - + +
156M ARG* 3.9 22.7 - - - +
163M GLY 3.2 19.0 + - - +
165M CYS* 1.3 77.8 - - - +
167M LEU* 1.3 72.2 + - + +
168M ASP 3.5 0.4 - - - -
171M TYR* 4.2 7.2 - - - -
172M LEU* 3.6 20.9 - - + +
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Residues in contact with LEU 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L GLU* 5.2 3.1 - - + +
68L GLY 5.8 0.4 - - - +
69L HIS* 3.0 48.5 - - + +
156M ARG* 4.2 14.6 - - - +
163M GLY 4.1 1.6 - - - +
164M ASN* 3.2 24.9 - - - +
165M CYS 2.6 5.1 + - - -
166M ILE* 1.3 91.4 - - + +
168M ASP* 1.3 55.6 + - - -
169M LYS* 3.4 14.6 + - - +
172M LEU* 4.7 5.3 - - - +
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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