Contacts of the helix formed by residues 156 - 171 (chain A) in PDB entry 1I4R
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 ALA 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL 3.5 2.5 + - - -
155A THR* 1.3 73.0 - - - +
157A GLN* 1.3 57.1 + - - +
159A LEU* 3.3 4.0 + - - +
160A ASP* 2.9 31.3 + - - +
188A PHE* 3.6 29.8 - - + -
196A PHE* 4.0 15.5 - - + -
198A TYR* 3.8 22.4 - - + +
221A LYS* 2.9 18.5 + - + +
222A THR* 4.3 0.4 - - - +
223A VAL* 4.7 5.2 - - + -
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR 4.8 0.2 - - - +
86A GLY* 3.2 10.0 - - - -
87A SER* 2.9 27.9 + - - +
111A MET* 5.0 0.2 - - - +
112A TYR 2.9 27.9 + - - +
114A GLY* 3.4 19.4 - - - +
155A THR* 3.8 9.4 - - - +
156A ALA* 1.3 79.9 - - - +
158A GLU* 1.3 61.6 + - - +
160A ASP* 3.4 0.7 + - - +
161A ILE* 3.0 38.4 + - + +
198A TYR* 5.4 0.2 + - - -
217A TYR* 3.3 59.3 + - + +
221A LYS 4.7 0.2 + - - -
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.4 46.3 + - + +
149A THR* 2.9 21.7 + - - -
150A ASP* 4.8 1.0 - - - +
151A LYS* 2.8 30.6 + - - -
154A VAL* 3.5 16.2 - - + +
155A THR* 3.1 20.8 + - - +
157A GLN* 1.3 79.8 - - - +
159A LEU* 1.3 62.6 + - + +
161A ILE* 3.6 1.6 + - - +
162A LYS* 3.1 53.0 + - + +
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Residues in contact with LEU 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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131A VAL* 4.2 13.9 - - + -
133A ILE* 5.1 0.7 - - - +
147A VAL* 4.2 23.9 - - + +
148A GLN 5.6 0.2 - - - -
149A THR* 4.5 11.2 - - - -
154A VAL* 3.6 37.7 - - + -
155A THR 4.0 3.4 - - - +
156A ALA 3.3 7.0 + - - +
158A GLU* 1.3 75.7 - - + +
160A ASP* 1.3 60.5 + - - +
162A LYS* 3.4 8.2 + - + +
163A ALA* 2.9 30.4 + - - +
188A PHE* 4.2 4.5 - - + -
223A VAL* 3.8 20.0 - - + -
228A VAL* 4.3 9.2 - - + -
230A ILE* 4.0 29.4 - - + -
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 4.7 0.2 - - - -
156A ALA 2.9 19.0 + - - +
157A GLN* 3.7 4.9 - - - +
159A LEU* 1.3 75.8 - - - +
161A ILE* 1.3 63.3 + - - +
163A ALA* 3.0 2.8 + - - +
164A ARG* 2.8 63.2 + - - +
186A ILE* 3.4 35.2 - - + +
188A PHE* 4.2 4.9 - - + -
198A TYR* 3.8 5.9 - - + -
217A TYR* 2.7 29.5 + - + +
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 5.0 0.2 - - - +
28A TYR* 3.7 36.9 - - + +
31A HIS 4.0 18.4 - - - +
32A TYR* 4.6 3.4 - - + -
85A TYR* 4.1 22.9 - - + +
86A GLY* 3.6 10.1 - - - -
87A SER* 3.4 34.8 - - - +
157A GLN* 3.0 35.1 + - + +
158A GLU 3.8 3.8 - - - +
160A ASP* 1.3 76.6 - - - +
162A LYS* 1.3 57.8 + - - +
164A ARG* 3.3 1.6 + - - +
165A ASN* 2.9 29.9 + - + +
217A TYR* 4.6 0.7 - - - +
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Residues in contact with LYS 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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85A TYR* 3.5 33.6 - - - +
147A VAL* 3.9 23.5 - - + +
148A GLN 2.6 32.2 + - - +
149A THR* 4.1 2.4 - - - +
158A GLU* 3.1 42.0 + - + +
159A LEU* 3.8 7.4 - - + +
160A ASP 3.3 0.2 - - - -
161A ILE* 1.3 76.7 - - - +
163A ALA* 1.3 61.8 + - - +
165A ASN* 3.5 7.9 + - - +
166A PHE* 3.3 21.1 + - - +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 4.4 21.5 - - + -
145A PHE* 3.6 20.5 - - + -
147A VAL* 4.0 1.9 - - - +
159A LEU 2.9 14.9 + - - +
160A ASP* 3.3 11.0 - - - +
162A LYS* 1.3 77.4 - - - +
164A ARG* 1.3 62.9 + - + +
166A PHE* 3.3 5.2 + - - +
167A LEU* 3.1 27.7 + - + +
186A ILE* 4.4 11.0 - - + -
232A VAL* 5.1 3.8 - - + -
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Residues in contact with ARG 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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24A MET* 4.3 0.4 - - - -
28A TYR* 3.4 47.0 + - + -
160A ASP* 2.8 56.1 + - - +
163A ALA* 1.3 70.7 - - + +
165A ASN* 1.3 60.5 + - - +
167A LEU* 3.8 2.1 - - - +
168A ILE* 2.9 37.0 + - - +
173A LEU* 4.1 11.6 - - + +
174A TYR* 3.0 28.3 + - + -
186A ILE* 4.2 4.8 - - + +
198A TYR* 4.2 2.6 - - - +
200A MET* 3.7 37.2 + - + +
213A TYR* 2.8 31.3 + - - -
216A MET* 3.7 10.5 - - - +
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR 3.2 15.0 + - - +
29A ASP* 3.7 6.5 + - - +
30A ASP* 2.7 40.5 - - - +
161A ILE* 2.9 17.7 + - + +
162A LYS* 3.7 9.4 - - - +
163A ALA 3.2 0.4 - - - -
164A ARG* 1.3 77.3 - - - +
166A PHE* 1.3 62.4 + - - +
168A ILE* 3.6 4.9 + - - +
169A ASN* 2.9 37.3 + - - +
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Residues in contact with PHE 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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143A ILE* 4.7 5.4 - - + -
145A PHE* 3.5 63.0 - + + -
146A GLU 5.8 0.9 - - - -
147A VAL* 5.6 0.4 - - + -
162A LYS 3.3 7.2 + - - +
163A ALA 3.3 8.9 + - - +
165A ASN* 1.3 82.3 + - - +
167A LEU* 1.3 61.4 + - + +
169A ASN* 3.2 7.7 + - - +
170A LYS* 2.8 64.0 + - + +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.9 18.2 - - + -
143A ILE* 4.3 2.9 - - + -
145A PHE* 3.8 22.7 - - + -
163A ALA 3.1 19.3 + - - +
164A ARG 3.4 3.8 + - - +
166A PHE* 1.3 81.4 - - + +
168A ILE* 1.3 60.9 + - - +
171A LYS* 2.8 48.6 + - + +
172A ASN 3.1 6.1 + - - -
173A LEU* 3.1 29.3 + - + -
200A MET* 4.6 3.1 - - + -
232A VAL* 4.0 37.5 - - + -
234A LEU* 5.1 3.1 - - + -
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Residues in contact with ILE 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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25A LYS* 3.9 37.2 - - + +
28A TYR* 3.7 39.0 - - + +
29A ASP* 3.8 15.7 - - + +
164A ARG 2.9 25.7 + - - +
165A ASN* 3.7 5.6 - - - +
166A PHE 3.2 0.2 - - - -
167A LEU* 1.3 77.7 - - - +
169A ASN* 1.3 63.8 + - - +
172A ASN* 3.1 26.5 + - - +
173A LEU* 3.7 10.3 - - + +
174A TYR* 3.9 30.3 - - + +
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Residues in contact with ASN 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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29A ASP* 4.5 11.3 + - - +
165A ASN* 2.9 35.8 + - - +
166A PHE* 3.2 7.3 + - - +
168A ILE* 1.3 84.4 - - - +
170A LYS* 1.3 61.4 + - - +
172A ASN* 4.0 8.7 - - - +
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Residues in contact with LYS 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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143A ILE* 4.2 16.8 - - + -
166A PHE* 2.8 51.6 + - + +
167A LEU* 4.6 0.2 - - - -
169A ASN* 1.3 75.3 - - + +
171A LYS* 1.3 81.2 + - + +
172A ASN* 3.7 0.4 - - - -
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Residues in contact with LYS 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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135A VAL* 5.7 2.5 - - + -
137A GLU* 3.2 36.6 + - - -
142A THR* 4.5 2.0 + - - -
143A ILE* 4.0 39.8 - - + +
167A LEU* 2.8 30.6 + - + +
170A LYS* 1.3 93.9 - - + +
172A ASN* 1.3 72.9 + - - +
173A LEU* 3.0 2.5 + - + +
180A PRO* 4.1 2.9 - - - +
181A TYR* 3.7 25.2 + - + +
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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
------------------------------------------------------------
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