Contacts of the helix formed by residues 156 - 170 (chain A) in PDB entry 5U03
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 SER 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PRO* 4.7 7.0 - - - -
147A LEU* 4.9 10.8 - - - -
148A GLY 4.2 19.1 - - - -
149A GLY* 5.1 0.9 - - - -
150A THR 3.8 15.1 + - - -
151A VAL* 5.3 0.9 - - - -
152A GLY 5.1 1.2 + - - -
153A ASP* 2.9 20.9 + - - +
155A GLU* 1.3 79.3 - - - +
157A MET* 1.3 64.1 + - - +
158A PRO* 3.3 4.0 - - - -
159A PHE* 2.9 25.2 + - - +
160A ILE* 3.1 18.4 + - - +
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Residues in contact with MET 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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152A GLY* 3.7 28.7 - - - +
153A ASP 3.5 10.1 - - - +
154A ILE* 3.1 29.6 + - + +
156A SER* 1.3 76.5 - - - +
158A PRO* 1.3 72.2 - - + +
160A ILE* 2.9 23.9 + - + +
161A GLU* 3.2 11.8 + - - +
207A LEU* 5.7 12.6 - - + -
154C ILE* 4.3 17.5 - - + -
157C MET* 5.7 4.9 - - - +
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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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90A THR* 6.4 1.1 - - + -
113A VAL* 4.1 31.4 - - + -
117A ILE* 4.8 6.7 - - + -
118A THR* 3.5 12.5 - - + +
121A ILE* 3.7 14.6 - - + +
154A ILE 3.4 10.3 - - - +
155A GLU 4.0 7.2 - - - +
156A SER 3.3 4.0 - - - -
157A MET* 1.3 97.2 - - + +
159A PHE* 1.3 61.2 + - + +
161A GLU* 3.5 2.1 + - + -
162A ALA* 3.1 21.5 + - - +
154C ILE* 5.1 7.8 - - + -
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Residues in contact with PHE 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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39A ILE* 3.5 37.0 - - + -
40A ASP 5.4 0.4 - - - -
41A PRO* 5.0 3.8 - - + -
88A LEU* 6.3 2.0 - - + -
89A THR 5.7 0.7 - - - -
90A THR* 3.8 32.1 - - + -
93A ILE* 3.9 16.8 - - + -
121A ILE* 3.6 38.8 - - + -
147A LEU* 4.0 16.2 - - + -
155A GLU 3.9 8.3 - - - -
156A SER* 2.9 23.7 + - - +
158A PRO* 1.3 80.2 - - + +
160A ILE* 1.3 66.3 + - - +
161A GLU 3.1 0.4 - - - -
162A ALA* 4.1 4.5 - - - -
163A PHE* 2.8 44.1 + + + -
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Residues in contact with ILE 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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7A THR* 5.4 3.4 - - + -
147A LEU* 4.4 19.7 - - + -
151A VAL* 5.5 6.7 - - + -
156A SER* 3.1 19.6 + - - +
157A MET* 2.9 16.5 + - + +
159A PHE* 1.3 76.7 - - - +
161A GLU* 1.3 56.0 + - - +
163A PHE* 3.8 2.1 - - - +
164A ARG* 2.8 28.4 + - + +
204A LEU* 4.7 5.2 - - + -
207A LEU* 3.8 50.9 - - + +
209A LEU* 3.8 29.6 - - + +
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Residues in contact with GLU 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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113A VAL* 5.8 0.7 - - + -
114A VAL* 3.8 30.7 - - + +
118A THR* 3.8 9.6 - - + +
157A MET 3.2 7.4 + - - +
158A PRO* 3.8 8.7 - - + +
159A PHE 3.1 0.2 - - - -
160A ILE* 1.3 78.2 - - - +
162A ALA* 1.3 69.2 + - - +
164A ARG* 2.7 52.8 + - - +
165A GLN* 3.1 13.0 + - + +
205D ARG* 5.8 0.3 + - - -
235D HIS* 4.1 10.6 + - - -
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Residues in contact with ALA 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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118A THR* 3.8 25.1 - - - +
121A ILE* 3.6 32.1 - - + -
122A GLN* 3.0 17.7 + - + +
158A PRO 3.1 13.5 + - - +
159A PHE 3.2 7.6 + - - +
161A GLU* 1.3 79.2 - - - +
163A PHE* 1.3 59.7 + - + +
165A GLN* 5.3 0.2 - - - -
166A PHE* 2.9 24.7 + - - +
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Residues in contact with PHE 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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5A LEU* 3.6 45.3 - - + -
39A ILE* 3.7 26.9 - - + -
121A ILE* 5.1 4.9 - - + -
125A VAL* 4.3 17.5 - - + -
145A ILE* 3.9 21.5 - - + -
147A LEU* 4.3 7.0 - - + -
159A PHE* 2.8 42.4 + + + +
160A ILE* 4.0 4.0 - - + +
162A ALA* 1.3 76.5 - - + +
164A ARG* 1.3 66.5 + - - +
166A PHE* 3.7 13.5 - + + -
167A GLN* 2.9 27.5 + - - +
175A PHE* 4.1 21.9 - + + -
209A LEU* 4.5 5.4 - - + -
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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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160A ILE* 2.8 20.0 + - + +
161A GLU* 2.7 45.5 + - - +
163A PHE* 1.3 77.7 - - - +
165A GLN* 1.3 89.8 + - - +
167A GLN* 3.1 8.6 + - - +
168A PHE* 3.0 47.0 - - + -
207A LEU 4.1 17.5 - - - +
208A GLY* 4.0 21.5 - - - +
209A LEU* 3.6 15.2 - - + +
205D ARG* 4.1 30.9 - - - +
235D HIS* 3.7 12.3 + - - -
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Residues in contact with GLN 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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122A GLN* 4.0 4.9 - - - +
161A GLU* 3.1 12.7 + - + +
162A ALA* 4.0 2.5 - - - +
164A ARG* 1.3 114.1 + - - +
166A PHE* 1.3 56.0 + - - +
168A PHE* 2.8 42.6 + - - +
169A LYS* 3.1 33.8 + - - +
205D ARG* 4.8 0.2 + - - -
235D HIS* 3.3 40.3 - - + +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.7 48.0 - + + -
122A GLN* 3.5 37.6 - - + +
125A VAL* 3.8 20.4 - - + -
126A MET* 4.8 9.6 - - + -
162A ALA 2.9 20.7 + - - +
163A PHE* 3.6 17.3 - + + +
165A GLN* 1.3 76.3 - - - +
167A GLN* 1.3 58.9 + - - +
169A LYS* 2.8 28.0 + - + +
170A VAL* 2.9 33.5 + - + +
175A PHE* 4.1 14.8 - + - -
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A PHE 2.9 11.6 + - - +
164A ARG* 3.1 22.1 + - - +
166A PHE* 1.3 75.8 - - - +
168A PHE* 1.3 83.1 + - + +
170A VAL* 2.9 28.6 - - - +
171A LYS 4.0 6.1 - - - +
172A ARG* 4.6 2.9 + - - -
175A PHE* 3.5 41.5 - - + +
177A ASN* 5.4 4.3 + - - +
208A GLY 4.0 7.1 + - - -
209A LEU* 3.5 27.4 - - - +
210A SER 5.5 3.7 + - - +
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ARG* 3.0 48.0 - - + -
165A GLN* 2.8 25.1 + - - +
167A GLN* 1.3 100.5 - - + +
169A LYS* 1.3 62.4 + - - +
170A VAL 3.2 8.0 - - - +
208A GLY 5.5 2.7 - - - -
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Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ASP* 4.1 12.1 + - - -
122A GLN* 2.7 39.7 + - - +
165A GLN* 3.1 28.5 + - - +
166A PHE* 2.8 13.0 + - + +
168A PHE* 1.3 77.4 - - - +
170A VAL* 1.3 63.6 + - + +
171A LYS* 5.5 3.6 - - - +
235D HIS* 6.2 0.9 - - - -
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Residues in contact with VAL 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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3A TYR* 3.9 12.6 - - + +
126A MET* 6.2 0.7 - - - -
166A PHE* 2.9 52.3 + - + +
167A GLN* 2.9 28.9 - - - +
168A PHE* 3.2 11.4 - - - +
169A LYS* 1.3 81.3 - - + +
171A LYS* 1.3 72.1 + - - +
172A ARG 3.9 0.2 + - - -
174A ASN* 4.2 14.8 - - + +
175A PHE* 3.9 13.0 - - + -
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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