Contacts of the helix formed by residues 158 - 172 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU* 2.8 14.3 + - + +
157A LYS* 1.3 79.5 + - + +
159A PRO* 1.3 56.0 - - - +
160A THR* 4.0 7.4 + - - -
161A ALA* 2.9 29.3 + - + +
162A PHE 2.7 31.2 + - - -
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Residues in contact with PRO 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.8 12.7 - - + +
156A TRP 3.9 8.4 - - - +
157A LYS 3.1 13.2 - - - +
158A ASN* 1.3 84.2 - - - +
160A THR* 1.3 56.9 + - - +
162A PHE* 3.0 8.0 + - + +
163A LYS* 2.6 40.3 + - - +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN* 3.3 7.9 + - - -
159A PRO* 1.3 82.0 - - - +
161A ALA* 1.3 63.8 + - - +
163A LYS* 3.5 7.1 + - - +
164A LYS* 3.1 23.1 + - + +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.9 19.1 - - + +
158A ASN* 2.9 29.9 + - + +
160A THR* 1.3 80.3 - - - +
162A PHE* 1.3 63.6 + - - +
164A LYS* 3.3 9.9 + - - +
165A TYR* 3.1 22.2 + - - +
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.1 15.9 - - + -
74A TYR* 3.5 25.6 - + - -
103A TYR* 3.5 30.5 - + - -
105A PRO* 4.5 5.2 - - + -
152A ALA* 3.6 18.8 - - + -
155A LEU* 3.7 19.0 - - + +
156A TRP* 3.6 45.5 - + + +
158A ASN 2.7 16.4 + - - +
159A PRO* 3.0 12.3 + - + +
161A ALA* 1.3 70.3 - - - +
163A LYS* 1.3 69.2 + - - +
165A TYR* 3.0 4.0 + - - +
166A LEU* 2.8 42.6 + - + -
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.4 50.7 + - + +
75A GLU* 4.8 15.8 + - - +
159A PRO 2.6 19.3 + - - +
160A THR* 3.6 7.6 - - - +
162A PHE* 1.3 75.0 - - - +
164A LYS* 1.3 57.8 + - - +
166A LEU* 3.3 7.1 + - + +
167A GLN* 2.7 68.0 + - - +
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR* 3.1 13.0 + - + +
161A ALA* 3.5 12.3 - - - +
162A PHE 3.1 0.2 - - - -
163A LYS* 1.3 81.7 - - - +
165A TYR* 1.3 62.4 + - - +
167A GLN* 3.4 5.9 + - - +
168A GLU* 3.0 27.1 + - + +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.9 29.9 - + + -
151A HIS* 3.6 28.9 + + - -
155A LEU* 3.6 25.8 - - + -
161A ALA 3.1 4.0 + - - +
162A PHE 3.0 2.7 + - - +
164A LYS* 1.3 79.3 - - - +
166A LEU* 1.3 53.3 + - - +
168A GLU* 3.3 9.0 + - + +
169A THR* 2.8 52.0 + - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.4 30.3 - - + +
74A TYR* 3.7 35.4 - - + +
77A LEU* 3.7 14.8 - - + -
79A TYR* 4.0 11.4 - - - +
103A TYR* 3.8 26.4 - - + +
162A PHE* 2.8 32.2 + - + +
163A LYS* 3.4 7.2 - - + +
165A TYR* 1.3 78.0 - - - +
167A GLN* 1.3 53.7 + - + +
169A THR* 2.8 22.8 - - + +
170A TYR* 2.8 23.7 + - + +
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL 5.4 0.8 + - - +
77A LEU* 5.3 13.2 - - + -
163A LYS* 2.7 61.4 + - + +
164A LYS* 3.9 5.7 - - - +
166A LEU* 1.3 75.8 - - + +
168A GLU* 1.3 58.0 + - - +
170A TYR* 3.7 6.2 - - - +
171A SER* 2.7 36.3 + - - -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS* 3.0 21.1 + - + +
165A TYR* 3.4 12.3 - - + +
167A GLN* 1.3 79.7 - - - +
169A THR* 1.3 63.2 + - - +
171A SER* 3.2 17.8 + - - -
172A LYS* 2.7 44.1 + - + +
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A TYR* 3.9 25.4 - - + +
165A TYR* 2.8 41.9 + - + +
166A LEU* 2.8 33.0 - - + +
168A GLU* 1.3 76.1 - - - +
170A TYR* 1.3 63.6 + - - +
172A LYS* 3.1 12.0 + - - +
173A GLN* 3.0 28.1 + - - +
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Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ASP 5.7 0.2 - - - -
77A LEU* 3.7 29.3 - - + -
78A ARG* 2.8 52.9 + - - +
79A TYR* 3.8 34.1 - + - -
100A THR* 4.6 7.3 - - + +
101A PRO 5.0 4.5 - - - -
166A LEU* 2.8 25.5 + - + +
167A GLN* 3.7 6.3 - - - +
169A THR* 1.3 74.0 - - + +
171A SER* 1.3 57.2 + - - +
173A GLN* 2.7 42.4 + - + +
174A VAL* 4.0 20.0 + - + +
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Residues in contact with SER 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN 2.7 23.7 + - - -
168A GLU* 3.2 10.3 - - - -
170A TYR* 1.3 76.3 - - - +
172A LYS* 1.3 62.5 + - - +
173A GLN 2.9 5.4 + - - -
174A VAL* 3.2 23.9 + - - +
175A THR* 3.8 9.5 + - - -
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 2.7 39.9 + - + +
169A THR* 3.1 13.1 + - - +
171A SER* 1.3 82.7 + - - +
173A GLN* 1.3 74.9 + - - +
174A VAL 3.6 1.6 - - - -
175A THR* 5.2 3.4 - - - -
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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