Contacts of the helix formed by residues 148 - 163 (chain A) in PDB entry 1Q1Z
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 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 1.3 74.3 - - - +
149A PRO* 1.3 71.7 - - - +
150A ARG* 2.8 50.2 + - - +
151A ASP* 3.1 17.5 + - - +
152A VAL* 3.0 18.5 + - - +
211A GLU* 3.2 18.8 + - - +
281A TRP* 4.1 19.4 - - - +
309A TRP* 3.4 35.5 + - + +
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Residues in contact with PRO 149 (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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147A ARG 3.1 9.2 - - - +
148A ASN* 1.3 87.4 - - - +
150A ARG* 1.3 57.5 + - - +
152A VAL* 3.2 10.1 + - + +
153A VAL* 2.9 34.5 + - - +
179A PHE* 4.1 5.1 - - + -
189A TRP* 3.4 49.8 - - + -
293A PHE* 3.6 26.5 - - + -
297A TYR* 3.9 9.6 - - + -
309A TRP* 3.7 12.6 - - - +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 2.8 32.1 + - - +
149A PRO* 1.3 79.5 - - - +
151A ASP* 1.3 60.6 + - - +
153A VAL* 3.0 19.3 + - - +
154A VAL* 3.2 11.4 + - - +
281A TRP* 3.5 61.0 - - + -
285A PHE* 3.7 17.1 - - + -
290A SER* 5.4 1.4 + - - +
293A PHE* 3.3 36.3 - - + -
294A ASP* 2.7 27.7 + - - -
297A TYR* 4.3 18.0 - - - -
309A TRP* 4.6 8.8 + - - -
310A ASP* 5.8 1.0 + - - -
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 3.8 26.1 + - - +
148A ASN* 3.1 24.3 + - + +
150A ARG* 1.3 75.7 - - - +
152A VAL* 1.3 64.2 + - - +
154A VAL* 3.3 6.9 + - - +
155A SER* 3.0 25.3 + - - -
210A TYR* 6.0 0.2 - - - -
211A GLU* 4.5 3.1 - - - +
274A ARG* 5.3 0.3 + - - -
277A VAL 4.9 0.4 - - - -
278A CYS* 3.9 8.4 - - - +
279A GLY* 3.0 22.9 + - - -
280A ASP* 3.2 7.9 + - + +
281A TRP* 3.0 37.5 + - - -
314A A3P 4.9 0.7 + - - -
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.9 21.5 - - + -
69A PRO 3.4 23.1 - - - +
70A LYS* 4.0 12.1 - - + +
71A SER* 3.7 12.1 - - - +
147A ARG* 3.7 29.6 - - + +
148A ASN 3.0 19.7 + - - +
149A PRO* 3.4 12.1 - - + +
151A ASP* 1.3 76.6 - - - +
153A VAL* 1.3 58.3 + - - +
155A SER* 3.8 1.1 - - - -
156A LEU* 2.8 31.2 + - + +
179A PHE* 4.3 7.9 - - + -
189A TRP* 4.6 3.4 - - + +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO 2.9 21.1 + - - +
150A ARG* 3.0 9.6 + - - +
152A VAL* 1.3 76.8 - - - +
154A VAL* 1.3 57.7 + - - +
156A LEU* 4.5 1.6 - - - -
157A TYR* 2.8 24.8 + - - +
175A PHE* 3.3 27.9 - - + -
176A LEU* 4.4 12.6 - - + -
179A PHE* 3.5 38.1 - - + -
284A HIS* 4.5 8.3 - - - +
285A PHE* 4.0 26.7 - - + -
293A PHE* 4.6 2.0 - - + -
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Residues in contact with VAL 154 (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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150A ARG 3.2 15.2 + - - +
151A ASP* 3.3 5.8 + - - +
153A VAL* 1.3 74.0 - - - +
155A SER* 1.3 66.0 + - - +
157A TYR* 3.1 15.0 + - - +
158A HIS* 3.1 33.3 + - + +
274A ARG* 4.0 4.7 - - - +
280A ASP* 3.6 23.8 - - + +
281A TRP* 3.4 30.5 - - + +
284A HIS* 3.7 32.5 - - + +
285A PHE* 4.3 0.7 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.4 28.1 - - - +
147A ARG* 3.9 6.1 - - - -
151A ASP 3.0 17.2 + - - -
152A VAL 3.8 3.1 - - - -
154A VAL* 1.3 76.5 - - - +
156A LEU* 1.3 57.4 + - - +
158A HIS* 3.6 1.6 + - - +
159A TYR* 3.0 31.1 + - - +
274A ARG* 4.2 6.0 + - - +
314A A3P 2.7 41.4 + - - -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 5.1 7.0 - - + +
69A PRO* 5.3 0.9 - - + -
70A LYS* 3.7 25.3 - - + +
152A VAL* 2.8 19.1 + - + +
153A VAL 3.7 4.0 - - - +
155A SER* 1.3 75.2 - - - +
157A TYR* 1.3 62.5 + - - +
159A TYR* 4.3 1.8 - - + -
160A SER* 2.7 42.8 + - - +
166A LEU* 4.1 10.1 - - + -
175A PHE* 3.5 21.5 - - + -
179A PHE* 4.4 21.1 - - + -
184A VAL* 4.7 15.9 - - + -
185A GLN* 3.7 26.7 - - + +
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Residues in contact with TYR 157 (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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153A VAL 2.8 14.7 + - - +
154A VAL 3.1 8.3 + - - +
156A LEU* 1.3 78.7 - - - +
158A HIS* 1.3 84.0 + + - +
160A SER 3.4 2.6 + - - -
161A LYS* 3.2 38.4 + - - +
169A PRO* 3.2 51.5 - - + +
170A GLY 3.6 15.5 + - - -
172A PRO* 3.8 30.0 - - + +
175A PHE* 3.8 25.7 - + + -
284A HIS* 3.6 26.5 - + + -
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 3.1 32.7 + - + +
155A SER 4.2 0.4 - - - +
157A TYR* 1.3 101.1 - + - +
159A TYR* 1.3 62.4 + - - +
161A LYS* 3.1 34.4 + - - +
162A ILE* 3.8 7.9 + - - +
274A ARG* 3.6 47.4 + - - -
280A ASP* 5.0 0.6 + - - -
284A HIS* 4.8 4.3 + - - -
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.3 35.9 - - + -
155A SER 3.0 20.1 + - - +
156A LEU* 3.9 3.8 - - + +
158A HIS* 1.3 77.4 - - - +
160A SER* 1.3 55.6 - - - +
161A LYS 3.1 0.7 + - - -
162A ILE* 3.1 14.3 + - + +
163A ALA* 2.8 47.7 + - + +
165A GLN* 3.5 20.2 + - - -
166A LEU* 3.7 20.2 - - + -
185A GLN* 5.2 4.0 - - - -
265A LEU* 4.1 18.8 - - + +
271A ALA 5.8 0.4 - - - -
272A PHE* 3.5 40.5 - + - -
274A ARG* 5.4 0.4 - - - +
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Residues in contact with SER 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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156A LEU* 2.7 28.7 + - - +
157A TYR 3.6 6.7 - - - -
158A HIS 3.2 0.4 - - - -
159A TYR* 1.3 76.9 - - - +
161A LYS* 1.3 55.3 + - - +
163A ALA 3.4 2.1 - - - +
166A LEU* 3.5 29.2 - - - +
167A LYS 3.7 17.3 - - - +
168A ASP* 4.7 0.3 - - - -
169A PRO* 3.7 15.9 - - - -
175A PHE* 4.5 6.8 - - - -
313A NA 2.4 30.7 - - - -
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Residues in contact with LYS 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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157A TYR* 3.2 48.9 + - - +
158A HIS* 3.1 25.4 + - - +
160A SER* 1.3 79.7 - - - +
162A ILE* 1.3 64.6 + - + +
168A ASP* 4.4 10.5 - - - +
169A PRO* 3.8 22.0 - - + -
170A GLY 5.8 0.2 - - - -
266A ASP* 5.4 0.9 - - - +
269A ARG* 6.0 0.2 - - - +
313A NA 3.8 6.0 - - - -
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Residues in contact with ILE 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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158A HIS 4.3 2.9 - - - +
159A TYR* 3.5 23.1 - - + +
161A LYS* 1.3 83.2 - - + +
163A ALA* 1.3 61.8 + - - +
164A GLY* 3.6 0.7 + - - -
264A LEU 4.2 0.2 - - - -
265A LEU* 3.2 27.2 - - + -
266A ASP* 3.0 50.4 + - - +
269A ARG* 3.9 16.8 - - + +
270A GLY* 3.7 36.6 - - - +
271A ALA 3.8 16.4 - - - +
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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
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159A TYR* 2.8 49.3 + - + +
161A LYS 3.5 0.4 - - - -
162A ILE* 1.3 77.3 - - - +
164A GLY* 1.3 59.0 + - - +
165A GLN* 3.4 12.1 - - - +
166A LEU* 3.1 17.3 + - + +
264A LEU 3.7 5.4 - - - +
265A LEU* 4.5 2.7 - - - -
313A NA 2.2 30.7 - - - -
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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
------------------------------------------------------------
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