Contacts of the helix formed by residues 159 - 169 (chain B) in PDB entry 1H9T
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 PRO 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A TRP* 2.8 44.1 - - + -
97A LEU* 6.0 1.1 - - + -
100A ASN* 4.3 15.7 - - - +
237A GLN 5.9 0.2 - - - +
238A GLY* 6.2 0.2 - - - -
239A ARG* 5.6 3.8 - - - +
154B PHE* 3.8 24.3 - - + +
157B GLY 2.8 23.1 - - - +
158B ASN* 1.3 74.6 - - - +
160B ILE* 1.3 70.3 + - + +
161B TYR 3.1 0.4 - - - -
162B GLY* 2.6 18.9 + - - +
163B LEU 3.1 4.0 + - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TRP* 5.0 2.9 - - + -
80A LEU* 3.8 21.8 - - + -
83A LEU* 4.5 20.0 - - + -
97A LEU* 4.2 10.1 - - + +
100A ASN* 3.8 10.5 - - + -
101A LEU* 3.2 50.7 - - + +
104A VAL* 4.2 20.9 - - + -
168A MET* 5.9 0.4 - - + -
158B ASN* 2.7 16.6 + - - +
159B PRO* 1.3 76.6 - - + +
161B TYR* 1.3 55.9 + - - +
163B LEU* 2.7 37.5 + - - +
164B ILE* 3.3 6.9 + - + +
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Residues in contact with TYR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A SER 3.1 7.8 + - - -
104A VAL* 3.8 12.5 - - + -
107A ASN* 3.0 34.1 + - - +
108A ILE* 4.2 27.6 - - + -
108B ILE* 4.2 21.5 - - + -
111B ILE* 4.0 9.1 - - + +
112B PHE* 4.0 30.3 - - + -
115B THR* 6.2 2.5 - - + -
153B ALA* 4.0 17.3 - - + -
156B SER* 4.1 3.6 - - - -
158B ASN* 3.1 47.9 + - + +
159B PRO 3.1 0.6 - - - -
160B ILE* 1.3 76.9 - - - +
162B GLY* 1.3 61.7 + - - +
164B ILE* 3.4 11.8 + - + +
165B LEU* 2.9 27.2 + - + +
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ARG* 5.2 1.9 - - - -
153B ALA* 4.0 13.7 - - - +
154B PHE* 3.9 25.7 - - - -
159B PRO* 2.6 19.1 + - - +
161B TYR* 1.3 70.9 - - - +
163B LEU* 1.3 52.0 + - - -
165B LEU* 3.2 3.7 + - - +
166B ASN* 2.4 43.0 + - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.8 1.8 - - + +
75A TRP* 4.3 40.8 - - + -
78A SER* 2.9 25.5 - - - +
79A GLY* 3.9 20.9 - - - +
80A LEU* 3.8 21.3 - - + +
82A ILE* 4.0 18.2 - - + -
83A LEU* 4.2 16.6 - - + -
159B PRO 3.1 6.1 + - - +
160B ILE* 2.7 19.6 + - - +
162B GLY* 1.3 70.9 - - - -
164B ILE* 1.3 50.2 + - - +
166B ASN* 2.7 9.9 - - + +
167B GLY* 2.6 32.1 + - - -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 6.0 0.2 - - - -
80A LEU* 4.0 22.9 - - + +
104A VAL* 5.0 5.8 - - + -
108A ILE* 4.1 20.0 - - + -
164A ILE* 3.5 46.0 - - + -
80B LEU* 3.7 15.7 - - + +
108B ILE* 4.5 11.7 - - + -
160B ILE* 3.9 11.4 - - + +
161B TYR* 3.5 14.8 - - + +
162B GLY 3.3 0.2 - - - -
163B LEU* 1.3 69.7 - - - +
165B LEU* 1.3 58.7 + - + +
166B ASN 2.7 4.3 - - - -
167B GLY* 2.5 22.7 + - - -
168B MET* 2.9 27.0 + - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 5.0 15.5 - - + +
108B ILE* 5.0 11.0 - - + -
112B PHE* 4.2 23.6 - - + -
146B TYR* 2.7 51.6 + - + -
149B PHE* 4.5 13.7 - - + -
150B ARG* 4.4 24.0 - - + +
153B ALA* 5.0 1.1 - - + -
161B TYR* 2.9 18.8 + - + +
162B GLY* 3.7 5.8 - - - +
164B ILE* 1.3 80.8 - - + +
166B ASN* 1.3 54.8 + - - +
168B MET* 3.5 28.9 + - + -
169B LYS 3.5 0.3 + - - -
172B TYR* 5.1 3.8 - - + -
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Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE 4.0 1.6 + - - -
75A TRP 4.0 8.3 + - - -
76A GLU* 2.9 30.1 + - - +
77A THR* 3.2 1.2 - - - +
78A SER 2.8 38.5 + - - +
146B TYR* 3.3 7.2 + - - -
150B ARG* 3.1 20.9 + - - +
162B GLY 2.4 19.0 + - - +
163B LEU* 2.7 17.5 - - - +
165B LEU* 1.3 76.5 - - - +
167B GLY* 1.3 59.0 + - - +
168B MET 3.3 0.5 + - - -
169B LYS* 3.5 18.7 + - - +
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Residues in contact with GLY 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A SER 5.7 0.4 - - - -
79A GLY* 5.2 10.1 - - - -
80B LEU* 3.9 31.0 - - - +
81B ASN* 4.7 5.4 + - - -
83B LEU* 4.6 1.2 - - - +
84B GLU* 5.1 5.9 - - - +
163B LEU 2.6 9.4 + - - -
164B ILE 2.5 15.2 + - - -
166B ASN* 1.3 73.4 - - - +
168B MET* 1.3 58.9 + - - -
170B GLY 4.9 1.8 + - - -
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ILE* 5.0 7.2 - - + -
164A ILE* 5.5 0.4 - - + -
80B LEU* 4.2 9.6 - - + -
83B LEU* 4.6 11.2 - - + -
101B LEU* 3.6 32.3 - - + -
104B VAL* 3.8 24.7 - - + -
105B ARG* 4.3 12.8 - - - +
108B ILE* 4.8 2.0 - - + -
164B ILE* 2.9 24.0 + - + +
165B LEU* 3.7 38.6 - - + +
166B ASN 3.2 0.4 - - - -
167B GLY* 1.3 80.3 - - - +
169B LYS* 1.3 66.5 + - - +
170B GLY 2.9 3.8 + - - -
171B LEU* 3.1 7.3 + - - +
172B TYR* 2.9 30.9 + - + -
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLU 5.2 7.8 + - - +
77A THR* 5.9 3.2 - - - +
143B GLU* 4.6 14.0 + - - -
146B TYR* 3.1 54.3 - - + +
150B ARG* 6.1 0.2 - - - +
165B LEU 3.5 4.6 + - - -
166B ASN* 3.6 13.0 - - - +
167B GLY 3.4 1.2 - - - -
168B MET* 1.3 75.1 - - - +
170B GLY* 1.3 70.5 + - - +
172B TYR* 4.4 0.4 - - - -
173B THR* 2.9 31.4 + - + +
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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