Contacts of the helix formed by residues 158 - 173 (chain B) in PDB entry 1I7K
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 ASN 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 2.9 15.0 + - + +
156B TRP 4.0 0.2 - - - -
157B LYS* 1.3 102.4 + - - +
159B PRO* 1.3 59.7 - - - +
160B THR* 3.2 22.3 + - - +
161B ALA* 3.1 23.7 + - + +
162B PHE* 2.9 24.3 + - - +
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Residues in contact with PRO 159 (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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73B VAL* 3.9 20.9 - - + +
156B TRP* 4.1 9.9 - - + +
157B LYS 3.3 11.9 - - - +
158B ASN* 1.3 87.1 - - - +
160B THR* 1.3 57.7 + - - +
162B PHE* 3.7 7.6 - - + +
163B LYS* 2.7 34.2 + - - +
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Residues in contact with THR 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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158B ASN* 3.2 12.8 + - - +
159B PRO* 1.3 80.1 - - - +
161B ALA* 1.3 61.7 + - - +
163B LYS* 3.9 4.8 - - - +
164B LYS* 3.2 23.3 + - + +
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Residues in contact with ALA 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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155B LEU* 3.5 22.1 - - + +
158B ASN* 3.1 23.8 + - + +
160B THR* 1.3 77.5 - - - +
162B PHE* 1.3 66.5 + - - +
164B LYS* 3.5 8.2 + - - +
165B TYR* 3.1 23.6 + - - +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.9 15.7 - - + -
74B TYR* 3.5 28.5 - + - -
103B TYR* 3.5 31.8 - + - -
105B PRO* 4.5 5.6 - - + -
152B ALA* 3.5 20.9 - - + -
155B LEU* 3.5 23.0 - - + +
156B TRP* 3.6 42.2 - + - +
158B ASN 2.9 16.8 + - - +
159B PRO* 3.7 8.5 - - + +
161B ALA* 1.3 77.2 - - - +
163B LYS* 1.3 62.7 + - - +
165B TYR* 3.2 3.5 + - - +
166B LEU* 2.9 36.3 + - + +
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Residues in contact with LYS 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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72B THR 4.8 4.7 - - - -
73B VAL* 3.9 40.2 + - + +
75B GLU* 4.8 14.1 + - - +
76B ASP* 5.7 1.6 + - - -
159B PRO 2.7 22.1 + - - +
160B THR* 3.9 5.2 - - - +
162B PHE* 1.3 72.8 - - - +
164B LYS* 1.3 62.1 + - - +
166B LEU* 3.4 6.2 + - - +
167B GLN* 3.0 63.3 + - + +
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Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR* 3.2 16.6 + - + +
161B ALA* 3.7 8.1 - - - +
163B LYS* 1.3 80.4 - - - +
165B TYR* 1.3 62.5 + - - +
167B GLN* 3.5 9.1 + - - +
168B GLU* 3.2 34.5 + - + +
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Residues in contact with TYR 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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103B TYR* 3.6 44.6 - + - -
151B HIS* 4.2 24.2 + + - -
155B LEU* 3.8 13.5 - - + -
161B ALA 3.1 15.2 + - - +
162B PHE 3.6 4.0 - - - +
164B LYS* 1.3 80.0 - - - +
166B LEU* 1.3 62.2 + - - +
168B GLU* 3.5 16.9 + - - +
169B THR* 3.0 54.0 + - + +
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Residues in contact with LEU 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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73B VAL* 3.4 29.2 - - + +
74B TYR* 3.6 37.5 - - + -
77B LEU* 3.6 13.9 - - + -
79B TYR* 3.9 10.5 - - - +
103B TYR* 3.7 29.4 - - + +
162B PHE* 2.9 31.1 + - + +
163B LYS* 3.5 4.9 - - + +
165B TYR* 1.3 80.9 - - - +
167B GLN* 1.3 56.8 + - + +
169B THR* 3.1 5.4 + - - +
170B TYR* 2.9 34.0 + - + +
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Residues in contact with GLN 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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73B VAL 5.9 0.7 - - - +
75B GLU 5.8 0.2 - - - +
77B LEU* 5.4 15.9 - - + +
163B LYS* 3.0 57.7 + - + +
164B LYS* 4.0 7.3 - - - +
166B LEU* 1.3 75.5 - - + +
168B GLU* 1.3 58.2 + - - +
170B TYR* 3.8 5.2 - - - +
171B SER* 2.9 34.0 + - - -
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Residues in contact with GLU 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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164B LYS* 3.2 25.6 + - + +
165B TYR* 3.6 23.7 - - - +
167B GLN* 1.3 79.9 - - - +
169B THR* 1.3 63.4 + - + +
171B SER* 3.1 12.9 + - - -
172B LYS* 3.1 30.0 + - + +
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Residues in contact with THR 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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103B TYR* 4.8 8.7 - - - +
165B TYR* 3.0 52.6 + - + +
166B LEU* 3.1 9.0 + - - +
168B GLU* 1.3 81.4 - - + +
170B TYR* 1.3 62.6 + - - +
172B LYS* 3.3 11.0 - - + +
173B GLN* 2.8 43.6 + - - +
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Residues in contact with TYR 170 (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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76B ASP 5.2 1.5 + - - -
77B LEU* 3.7 27.7 - - + -
78B ARG* 2.9 47.2 + - - +
79B TYR* 4.1 30.1 - + - -
100B THR* 4.3 11.6 - - + +
101B PRO 5.0 3.6 - - - -
166B LEU* 2.9 22.8 + - + +
167B GLN* 3.8 5.6 - - - +
169B THR* 1.3 76.2 + - - +
171B SER* 1.3 64.4 + - - +
173B GLN* 2.9 32.8 + - + +
174B VAL* 3.3 24.9 - - + +
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Residues in contact with SER 171 (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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167B GLN 2.9 19.6 + - - -
168B GLU* 3.1 10.0 + - - -
170B TYR* 1.3 75.8 - - - +
172B LYS* 1.3 53.2 + - - +
173B GLN 2.4 22.4 - - - +
174B VAL* 4.0 7.2 - - - -
175B THR* 2.6 29.4 + - - +
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLU* 3.1 26.0 + - + +
169B THR* 3.3 14.6 - - + +
171B SER* 1.3 76.5 + - - +
173B GLN* 1.3 70.2 + - - +
175B THR* 3.2 20.0 + - - +
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Residues in contact with GLN 173 (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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100B THR* 6.3 0.7 - - + -
101B PRO* 3.9 42.4 - - + +
169B THR* 2.8 31.8 + - - +
170B TYR* 2.9 16.8 + - + +
171B SER 2.4 21.7 - - - +
172B LYS* 1.3 76.8 - - - +
174B VAL* 1.3 56.8 + - + +
175B THR 2.4 21.8 + - - -
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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