Contacts of the helix formed by residues 158 - 167 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76R ASN* 3.4 14.5 + - - +
81R TYR* 3.9 23.1 - + - +
43S LEU* 3.3 34.2 - - + +
79S PHE* 4.1 15.9 - + + -
113S VAL* 4.0 26.7 - - + -
115S LEU* 3.3 46.7 - - + -
119S SER* 4.5 4.5 - - - -
120S TYR* 4.7 12.1 - - - -
121S HIS* 3.6 28.9 - + - -
154S ALA 4.9 0.2 - - - -
155S LEU* 3.0 29.0 + - + +
156S ARG 3.0 0.4 + - - -
157S SER* 1.3 77.6 - - - +
159S GLY* 1.3 57.4 + - - +
162S LEU* 4.7 3.6 - - + -
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Residues in contact with GLY 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R ASN* 4.4 3.8 - - - -
76R ASN* 3.9 10.1 - - - -
43S LEU* 3.9 8.7 - - - -
155S LEU 4.3 0.4 + - - -
156S ARG 3.0 7.7 + - - +
157S SER 3.2 1.2 - - - -
158S PHE* 1.3 81.2 - - - +
160S ASN* 1.3 67.6 + - - -
161S ALA 3.3 2.7 - - - -
162S LEU* 3.0 13.3 + - - +
163S GLY 3.4 0.9 + - - -
164S ASN* 3.1 21.7 + - - +
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Residues in contact with ASN 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R HIS* 6.0 0.3 - - - -
73R ASN* 3.1 32.4 + - - +
43S LEU 3.1 4.2 + - - +
44S ARG* 3.0 25.3 + - - +
45S GLN 3.1 16.6 - - - +
46S ARG* 4.2 17.4 + - - +
47S LEU* 3.0 12.0 - - - +
159S GLY* 1.3 69.5 - - - -
161S ALA* 1.3 59.1 + - - +
163S GLY* 2.7 22.2 + - - -
164S ASN* 3.5 8.8 + - - +
165S CYS* 3.6 29.6 + - + +
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Residues in contact with ALA 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192R LYS* 4.4 12.8 - - + -
42S ALA 3.4 25.6 - - - +
43S LEU* 2.9 14.9 + - + +
45S GLN* 2.8 14.6 + - + +
47S LEU* 3.8 9.7 - - - +
74S LEU* 3.6 24.1 - - - +
78S MET* 3.8 15.9 - - + -
160S ASN* 1.3 74.9 - - - +
162S LEU* 1.3 62.3 + - - +
163S GLY 3.4 1.1 + - - -
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Residues in contact with LEU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43S LEU* 3.7 23.8 - - + -
66S ILE* 5.0 3.7 - - - +
71S VAL* 4.3 13.6 - - + +
74S LEU* 4.0 15.0 - - + -
75S ALA* 3.9 27.6 - - + +
78S MET* 4.1 23.1 - - + -
79S PHE* 4.5 9.4 - - + -
152S LYS 4.7 1.2 - - - +
155S LEU* 3.5 41.2 - - + +
156S ARG* 3.8 14.5 + - - +
158S PHE* 4.7 2.7 - - + -
159S GLY 3.0 14.4 + - - +
160S ASN 2.8 0.2 + - - -
161S ALA* 1.3 83.5 - - - +
163S GLY* 1.3 57.5 + - - +
164S ASN 3.8 0.2 - - - -
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Residues in contact with GLY 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S LEU* 4.3 3.9 - - - +
66S ILE* 3.8 23.3 - - - +
156S ARG* 3.7 14.8 - - - -
160S ASN 2.7 8.6 + - - -
161S ALA 3.4 1.6 + - - -
162S LEU* 1.3 81.1 - - - +
164S ASN* 1.3 62.8 + - - +
165S CYS 3.1 4.2 + - - -
166S ILE* 3.2 25.2 + - - +
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Residues in contact with ASN 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R HIS* 3.0 44.3 - - - +
72R ILE* 3.5 31.6 - - - +
73R ASN* 3.3 19.8 + - - +
156S ARG* 3.3 20.5 + - - +
159S GLY* 3.1 25.5 + - - +
160S ASN* 3.5 3.5 + - - +
162S LEU 3.8 0.6 - - - -
163S GLY* 1.3 76.4 - - - +
165S CYS* 1.3 61.3 + - - +
167S LEU* 3.2 16.9 - - - +
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Residues in contact with CYS 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R HIS* 5.7 0.4 - - - -
46S ARG* 3.9 27.6 - - - +
47S LEU* 3.2 40.2 - - - -
52S ILE* 5.8 0.2 - - - -
160S ASN* 3.6 18.2 + - + +
163S GLY* 3.1 2.8 - - - -
164S ASN* 1.3 75.4 - - - +
166S ILE* 1.3 62.3 + - - +
167S LEU 2.7 4.2 + - - -
168S ASP* 2.6 42.5 + - - +
171S TYR* 3.6 30.6 - - + -
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Residues in contact with ILE 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S ILE* 4.4 11.4 - - + -
64S CYS* 3.3 43.2 - - + +
65S TYR* 3.6 7.4 - - - +
66S ILE* 3.9 28.3 - - + -
156S ARG* 3.9 22.9 - - - +
163S GLY 3.2 19.2 + - - +
165S CYS* 1.3 78.4 - - - +
167S LEU* 1.3 72.3 + - + +
168S ASP 3.5 0.2 - - - -
171S TYR* 4.1 8.1 - - - -
172S LEU* 3.6 20.6 - - + +
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Residues in contact with LEU 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R GLU* 5.2 2.9 - - + +
68R GLY* 5.7 1.1 - - - +
69R HIS* 3.2 45.9 + - + +
156S ARG* 4.2 15.0 - - - +
163S GLY 4.1 1.6 - - - +
164S ASN* 3.2 24.9 - - - +
165S CYS 2.7 2.4 + - - -
166S ILE* 1.3 90.4 - - + +
168S ASP* 1.3 62.5 + - - +
169S LYS* 3.3 13.2 + - - +
172S LEU* 4.6 5.9 - - - +
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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