Contacts of the helix formed by residues 142 - 162 (chain A) in PDB entry 5GUF
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 THR 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.0 27.6 - - + +
11A ILE 3.0 6.4 + - - +
12A ASP* 3.9 23.8 - - + -
140A THR* 6.0 1.1 - - + -
141A TRP* 1.3 76.8 - - - +
143A PRO* 1.3 73.4 - - + +
144A ARG* 3.9 5.8 + - - +
145A VAL* 3.3 29.3 + - - +
146A ALA* 2.9 21.3 + - - +
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Residues in contact with PRO 143 (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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141A TRP 3.8 4.5 - - - +
142A THR* 1.3 86.5 - - + +
144A ARG* 1.3 62.3 + - - +
146A ALA* 3.2 8.5 + - + +
147A VAL* 2.9 31.0 + - + +
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Residues in contact with ARG 144 (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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142A THR* 3.2 6.1 + - - +
143A PRO* 1.3 78.4 - - - +
145A VAL* 1.3 62.3 + - + +
147A VAL* 3.2 7.3 + - - +
148A GLU* 2.8 55.1 + - + +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 4.0 17.3 - - + +
12A ASP 3.4 28.0 - - - +
13A ASN* 3.6 17.5 - - - +
14A ILE* 4.4 2.9 - - - +
17A ALA* 3.8 25.6 - - + -
141A TRP* 4.0 2.2 - - + -
142A THR* 3.2 17.7 + - - +
144A ARG* 1.3 79.6 - - + +
146A ALA* 1.3 59.9 + - - +
148A GLU* 3.8 17.7 - - - +
149A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 146 (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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127A TYR* 2.6 30.9 + - - +
131A LEU* 4.7 12.1 - - + -
141A TRP* 3.8 19.0 - - + -
142A THR 2.9 14.0 + - - +
143A PRO* 3.2 12.8 + - + +
145A VAL* 1.3 77.9 - - - +
147A VAL* 1.3 61.6 + - + +
150A ALA* 3.3 10.4 + - - +
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Residues in contact with VAL 147 (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 PRO* 2.9 20.8 + - + +
144A ARG* 3.2 8.5 + - - +
146A ALA* 1.3 76.2 - - + +
148A GLU* 1.3 66.9 + - + +
150A ALA* 3.1 8.4 + - + +
151A ALA* 2.9 23.8 + - + +
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Residues in contact with GLU 148 (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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14A ILE* 3.8 31.7 + - + +
144A ARG* 2.8 55.4 + - + +
145A VAL* 3.8 15.7 - - - +
147A VAL* 1.3 73.9 - - + +
149A ALA* 1.3 51.2 + - - +
151A ALA* 3.1 9.1 + - - +
152A ALA* 2.7 35.2 + - - +
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Residues in contact with ALA 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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14A ILE* 3.5 17.4 - - + +
17A ALA* 4.2 6.3 - - + -
18A ILE* 5.9 2.0 - - + -
21A MET* 5.4 2.7 - - + -
127A TYR* 3.3 27.6 - - + +
141A TRP* 4.1 11.4 - - + -
145A VAL 3.0 14.9 + - - +
148A GLU* 1.3 75.2 - - - +
150A ALA* 1.3 58.5 + - - +
152A ALA* 3.1 5.1 + - - +
153A VAL* 2.8 32.7 + - + +
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Residues in contact with ALA 150 (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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124A LEU* 3.7 20.9 - - + +
127A TYR* 3.6 22.8 + - + -
146A ALA 3.3 12.8 + - - +
147A VAL* 3.1 12.4 + - + +
149A ALA* 1.3 76.5 - - - +
151A ALA* 1.3 57.9 + - - +
153A VAL* 3.2 6.3 + - - +
154A LEU* 3.0 31.2 + - + +
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Residues in contact with ALA 151 (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 VAL* 2.9 16.9 + - + +
148A GLU* 3.6 9.6 - - - +
150A ALA* 1.3 73.2 - - - +
152A ALA* 1.3 60.5 + - - +
154A LEU* 3.4 14.4 + - + +
155A LEU* 2.8 38.8 + - + +
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Residues in contact with ALA 152 (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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14A ILE* 4.5 13.2 - - + -
18A ILE* 4.9 11.4 - - + -
148A GLU 2.7 17.6 + - - +
149A ALA* 3.1 13.2 + - - +
151A ALA* 1.3 71.6 - - - +
153A VAL* 1.3 64.1 + - + +
155A LEU* 3.9 11.5 - - + +
156A LEU* 3.0 24.8 + - - +
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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
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21A MET* 6.5 0.7 - - + -
25A MET* 5.0 15.0 - - + -
123A GLN* 3.3 27.8 - - + +
124A LEU* 4.0 7.6 - - + -
126A PHE* 3.9 20.4 - - + -
127A TYR* 4.3 18.8 - - + -
149A ALA* 2.8 18.2 + - + +
150A ALA 3.2 8.3 + - - +
152A ALA* 1.3 73.5 - - + +
154A LEU* 1.3 65.6 + - - +
156A LEU* 3.3 6.4 + - - +
157A HIS* 3.0 37.5 + - + -
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Residues in contact with LEU 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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120A LEU* 4.1 28.7 - - + -
123A GLN* 3.8 29.8 - - + +
124A LEU* 4.3 15.3 - - + -
150A ALA* 3.0 17.4 + - + +
151A ALA* 3.6 15.5 - - + +
152A ALA 3.3 0.2 - - - -
153A VAL* 1.3 75.9 - - - +
155A LEU* 1.3 63.9 + - + +
157A HIS* 3.2 4.1 + - - +
158A LEU* 2.9 39.6 + - + +
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Residues in contact with LEU 155 (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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151A ALA* 2.8 31.6 + - + +
152A ALA* 3.9 8.5 - - - +
153A VAL 3.3 0.2 - - - -
154A LEU* 1.3 74.5 - - + +
156A LEU* 1.3 52.6 + - - +
158A LEU* 3.5 7.5 - - + +
159A ALA* 2.6 34.7 + - - +
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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
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25A MET* 4.4 25.4 - - + -
152A ALA 3.0 18.9 + - - +
153A VAL* 3.9 4.9 - - - +
154A LEU 3.2 0.2 - - - -
155A LEU* 1.3 74.1 - - - +
157A HIS* 1.3 63.9 + - + +
159A ALA* 3.6 12.1 - - + -
160A ALA* 2.4 41.5 + - + +
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Residues in contact with HIS 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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28A ASN* 4.3 21.4 + - - -
122A ASP 4.9 3.4 - - - -
123A GLN* 3.8 36.3 + - + +
126A PHE* 4.3 5.5 - - - -
153A VAL* 3.0 41.7 + - + +
154A LEU 3.6 3.8 - - - +
156A LEU* 1.3 83.9 - - + +
158A LEU* 1.3 65.8 + - + +
160A ALA* 3.2 10.3 + - - +
161A ASN* 3.1 25.8 + - - +
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Residues in contact with LEU 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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123A GLN* 5.8 3.8 - - + -
154A LEU* 2.9 43.1 + - + +
155A LEU* 4.0 7.4 - - + +
157A HIS* 1.3 80.7 - - + +
159A ALA* 1.3 57.1 + - - +
161A ASN* 3.8 6.8 - - - +
162A ILE* 3.0 38.8 + - + +
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Residues in contact with ALA 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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155A LEU 2.6 24.3 + - - +
156A LEU* 2.9 19.7 + - + +
158A LEU* 1.3 74.2 - - - +
160A ALA* 1.3 62.8 + - - +
162A ILE* 3.1 30.1 - - + +
163A THR* 3.2 14.7 - - + +
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Residues in contact with ALA 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* 2.4 34.2 + - + +
157A HIS* 3.2 10.3 + - - +
159A ALA* 1.3 68.9 - - - +
161A ASN* 1.3 65.7 + - - +
163A THR* 3.3 23.1 + - - -
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Residues in contact with ASN 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 HIS 3.1 16.0 + - - +
158A LEU* 4.1 6.5 - - - +
159A ALA 3.2 0.2 - - - -
160A ALA* 1.3 80.5 - - - +
162A ILE* 1.3 59.5 + - + +
163A THR 3.1 11.4 + - - +
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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 LEU* 3.0 16.2 + - + +
159A ALA* 3.1 30.3 - - + +
161A ASN* 1.3 75.0 - - + +
163A THR* 1.3 65.5 + - + +
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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