Contacts of the helix formed by residues 157 - 169 (chain A) in PDB entry 1QQW
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 ASP 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ILE* 3.7 6.7 - - - +
156A ARG* 1.3 81.7 - - + +
158A PRO* 1.3 75.1 - - - +
159A ILE* 3.1 24.1 + - - +
160A LEU* 3.1 32.8 + - + +
349A LYS* 4.2 11.8 - - + +
350A MET* 3.5 4.8 - - - -
434A THR* 4.1 10.1 + - - +
39D LEU 4.0 1.3 - - - +
40D ASN* 3.0 32.8 - - - +
41D VAL* 3.4 16.4 + - - +
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Residues in contact with PRO 158 (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 ASP* 1.3 90.7 - - - +
159A ILE* 1.3 59.2 + - - +
160A LEU 2.9 6.3 + - - -
161A PHE* 3.0 14.6 + - - +
162A PRO* 3.3 10.0 - - - +
349A LYS* 3.2 41.7 - - + +
350A MET* 3.3 12.5 - - - +
353A GLY* 4.3 9.6 - - - +
600A HEM 4.0 19.1 - - + -
41D VAL* 4.7 10.3 - - + -
50D LEU* 5.8 0.4 - - + -
57D PHE* 4.0 21.8 - - + -
61D MET* 3.9 5.9 - - + +
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Residues in contact with ILE 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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157A ASP* 3.1 17.0 + - - +
158A PRO* 1.3 77.4 - - - +
160A LEU* 1.3 63.5 + - + +
162A PRO* 3.8 8.2 - - - +
431A ARG* 4.8 0.9 - - - +
38D LYS* 3.1 52.8 + - + +
39D LEU* 3.3 26.0 - - - +
40D ASN* 3.5 11.4 - - - +
41D VAL* 4.6 3.1 - - + +
54D ASP* 4.6 4.9 - - - +
56D VAL* 4.4 9.9 - - + -
57D PHE* 3.5 49.9 - - + +
60D GLU* 4.1 9.0 - - - +
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Residues in contact with LEU 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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155A ILE* 3.8 15.0 - - + -
157A ASP* 3.1 37.3 + - + +
158A PRO 3.0 1.2 - - - -
159A ILE* 1.3 82.0 - - + +
161A PHE* 1.3 67.2 + - - +
162A PRO* 3.3 3.1 - - - -
163A SER* 3.0 11.8 + - - -
164A PHE* 2.8 19.9 + - - +
185A PHE* 4.1 17.2 - - + -
189A ARG* 3.6 49.4 - - - +
191A GLU* 4.4 7.0 - - - +
405B TYR 4.2 10.3 - - - +
406B PRO* 4.4 1.8 - - + -
38D LYS* 4.6 1.1 - - - +
39D LEU* 4.1 19.5 - - + +
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Residues in contact with PHE 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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74A VAL* 4.3 9.9 - - + -
75A HIS* 6.1 1.8 - - - -
153A PHE* 4.1 22.2 - + - -
155A ILE* 3.4 15.7 - - + +
158A PRO* 3.0 9.8 + - + +
160A LEU* 1.3 77.5 - - - +
162A PRO* 1.3 72.4 - - + +
164A PHE* 3.0 3.4 + + - -
165A ILE* 2.9 62.1 + - + +
600A HEM 3.4 73.6 - + + -
61D MET* 4.6 2.2 - - + -
64D PHE* 3.7 24.7 - + - -
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Residues in contact with PRO 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 PRO 3.3 10.5 - - - +
159A ILE* 3.8 5.6 - - - +
160A LEU 3.4 4.3 - - - -
161A PHE* 1.3 96.1 - - + +
163A SER* 1.3 62.4 + - - +
165A ILE* 3.4 2.4 + - - +
166A HIS* 3.1 32.2 + - + +
386B TYR 6.0 1.3 - - - +
57D PHE* 6.0 0.4 - - + -
60D GLU* 4.0 31.2 - - + +
61D MET* 3.9 25.1 - - + +
64D PHE* 4.0 29.4 - - + -
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Residues in contact with SER 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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160A LEU 3.0 8.6 + - - -
162A PRO* 1.3 77.5 - - - +
164A PHE* 1.3 64.2 + - - +
166A HIS* 2.9 16.6 + - - +
167A SER* 2.9 11.8 + - - -
185A PHE* 4.4 3.6 - - - -
386B TYR* 5.4 2.7 - - - +
403B ASN 4.3 2.2 - - - -
404B TYR* 3.5 14.8 - - - +
405B TYR 3.4 33.8 + - - -
38D LYS* 3.0 29.3 + - - -
60D GLU* 4.2 2.8 + - - -
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Residues in contact with PHE 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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116A VAL* 5.9 3.4 - - + -
153A PHE* 4.1 18.4 - + - -
154A PHE* 3.3 41.5 - + + -
155A ILE* 4.4 5.6 - - + -
160A LEU 2.8 16.7 + - - +
161A PHE* 3.0 12.1 + + - +
163A SER* 1.3 72.9 - - - +
165A ILE* 1.3 84.6 + - + +
167A SER* 2.9 23.0 + - - -
168A GLN* 3.1 35.0 + - + +
185A PHE* 3.3 36.9 - + + -
186A TRP* 3.5 25.4 - + - -
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Residues in contact with ILE 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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73A VAL* 4.5 1.1 - - + +
74A VAL* 3.4 26.7 - - + -
116A VAL* 4.5 14.8 - - + -
117A ALA* 6.0 1.3 - - - -
153A PHE* 5.5 0.7 - - + -
161A PHE* 2.9 61.0 + - + +
162A PRO 3.9 3.6 - - - +
164A PHE* 1.3 92.3 - - + +
166A HIS* 1.3 64.5 + - + +
168A GLN* 3.5 7.6 + - + +
169A LYS* 2.9 39.9 + - + +
64D PHE* 4.2 14.1 - - + -
68D ARG* 5.5 0.9 - - - +
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Residues in contact with HIS 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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162A PRO* 3.1 24.5 + - + -
163A SER* 2.9 11.3 + - - +
165A ILE* 1.3 78.3 - - + +
167A SER* 1.3 58.0 + - - +
169A LYS* 3.0 25.5 + - + +
170A ARG 4.3 1.0 - - - +
181A MET* 3.4 12.5 - - - +
386B TYR 3.3 21.9 + - - -
387B GLN* 4.9 0.2 - - - -
388B ARG* 4.5 12.5 - - + +
403B ASN* 2.6 50.3 + - + +
64D PHE* 4.2 7.2 - + + -
67D GLU* 2.7 39.4 + - - -
68D ARG* 6.0 0.9 - - - -
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Residues in contact with SER 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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163A SER 2.9 10.2 + - - -
164A PHE* 2.9 19.6 + - - -
166A HIS* 1.3 77.7 - - - +
168A GLN* 1.3 63.4 + - - +
169A LYS 3.4 3.6 + - - +
178A ASP 4.6 0.2 - - - +
181A MET* 3.3 38.0 - - - +
182A VAL* 3.4 27.9 + - - +
185A PHE* 4.0 16.4 - - - +
404B TYR* 4.1 15.9 - - - +
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Residues in contact with GLN 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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116A VAL* 6.2 3.9 - - + +
117A ALA* 3.8 25.7 - - + +
128A ASP* 4.5 14.6 + - - -
129A PRO* 6.0 0.4 - - - +
154A PHE* 5.9 1.0 - - - -
164A PHE* 3.1 44.9 + - + +
165A ILE* 3.7 11.4 - - + +
166A HIS 3.2 0.2 - - - -
167A SER* 1.3 84.4 + - - +
169A LYS* 1.3 61.8 - - + +
177A LYS* 4.2 13.0 + - - +
182A VAL* 3.5 32.6 - - - +
186A TRP* 3.6 21.3 - - - -
199A LEU* 5.7 3.6 - - - +
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Residues in contact with LYS 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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71A GLU* 5.1 4.0 + - - -
72A ARG 5.1 1.4 + - - -
73A VAL 3.2 22.2 + - - -
74A VAL* 4.6 0.6 - - - +
76A ALA* 5.5 1.8 - - - +
116A VAL 4.2 6.5 + - - -
117A ALA* 3.2 36.5 + - + +
118A GLY 5.0 2.2 + - - -
119A GLU* 4.1 17.2 + - - +
165A ILE* 2.9 32.3 - - + +
166A HIS* 3.0 12.7 + - + +
167A SER 3.8 6.9 - - - +
168A GLN* 1.3 83.5 - - - +
170A ARG* 1.3 71.1 + - + +
171A ASN 4.1 0.3 + - - -
177A LYS* 4.1 19.4 - - - +
178A ASP 4.3 3.6 + - - -
181A MET* 4.7 1.7 - - - +
182A VAL* 5.7 0.2 - - - +
68D ARG* 3.1 33.4 - - - +
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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