Contacts of the helix formed by residues 138 - 154 (chain A) in PDB entry 2DFS
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 HIS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TYR* 3.2 30.6 - + - -
102A TYR* 4.5 0.2 + - - -
107A LEU* 3.7 15.5 - - - +
118A ILE* 3.1 51.0 - - + +
119A TYR* 4.1 13.2 - + - -
123A ILE* 4.9 3.1 - - + -
127A TYR* 3.4 31.7 - - + +
136A ASP 3.4 1.4 + - - -
137A PRO* 1.3 76.6 - - - +
139A ILE* 1.4 63.8 + - - +
140A PHE* 3.5 27.6 + + - +
141A ALA* 3.2 14.9 + - - +
142A VAL* 3.4 10.0 + - - +
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Residues in contact with ILE 139 (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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100A TYR* 3.5 29.6 - - + +
107A LEU* 3.8 9.5 - - + +
119A TYR* 4.1 10.5 - - + -
138A HIS* 1.4 73.6 - - - +
140A PHE* 1.3 65.7 + - + +
142A VAL* 3.4 7.0 + - + +
143A ALA* 3.1 25.7 + - - +
159A ILE* 5.5 4.3 - - + -
161A VAL* 5.7 1.3 - - + -
172A SER* 3.6 37.5 - - - +
175A TYR* 4.1 20.9 - - + -
176A ALA* 4.4 14.4 - - + +
659A VAL* 3.8 29.4 - - + -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE 3.6 18.6 - - - -
119A TYR* 3.7 29.4 - + + -
123A ILE* 4.1 7.9 - - + -
124A ILE* 3.6 35.2 - - + -
127A TYR* 3.8 25.6 - + + -
138A HIS* 3.5 17.5 - - - +
139A ILE* 1.3 79.8 - - + +
141A ALA* 1.4 58.0 + - - +
143A ALA* 3.2 5.7 + - + +
144A GLU* 2.9 29.5 + - - +
175A TYR* 3.7 35.9 - + + -
178A ARG* 5.8 0.4 - - + -
179A TYR* 3.6 31.0 - + + -
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Residues in contact with ALA 141 (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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102A TYR* 3.9 21.5 - - - +
127A TYR* 4.0 23.5 - - + -
132A MET* 4.4 17.5 - - + +
135A MET* 5.6 1.3 - - + -
136A ASP 4.6 0.4 - - - +
138A HIS 3.2 19.0 + - - +
140A PHE* 1.4 78.1 - - - +
142A VAL* 1.3 63.3 + - + +
144A GLU* 3.5 6.5 + - - +
145A GLU* 3.2 25.3 + - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 5.3 3.1 - - + -
107A LEU* 3.9 30.3 - - + -
132A MET* 5.0 13.0 - - + -
138A HIS 3.4 12.2 + - - +
139A ILE* 3.7 12.3 - - + +
140A PHE 3.4 0.2 - - - -
141A ALA* 1.3 75.7 - - + +
143A ALA* 1.4 60.4 + - - +
145A GLU* 3.5 6.6 + - - +
146A ALA* 3.2 21.1 + - - +
159A ILE* 4.4 17.4 - - + +
657A HIS* 3.9 27.6 + - + +
658A TYR 5.0 3.8 - - - +
659A VAL* 4.4 8.1 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE 3.1 14.4 + - - +
140A PHE* 3.2 9.2 + - - +
142A VAL* 1.4 72.9 - - - +
144A GLU* 1.3 63.4 + - - +
146A ALA* 3.3 2.3 + - - +
147A TYR* 3.1 18.4 + - - +
159A ILE* 4.4 4.0 - - - +
176A ALA* 4.3 9.4 - - + +
179A TYR* 3.5 28.9 - - + -
180A PHE* 3.2 34.1 - - + -
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Residues in contact with GLU 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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127A TYR* 3.8 12.3 - - + +
128A SER* 3.6 3.1 + - - -
129A GLY* 3.0 33.9 + - - -
130A GLN 3.8 4.5 - - - +
140A PHE 2.9 13.2 + - - +
141A ALA* 3.6 8.3 - - - +
143A ALA* 1.3 73.3 - - - +
145A GLU* 1.3 57.8 + - - +
147A TYR* 3.3 14.7 + - - +
148A LYS* 2.9 56.1 + - - +
179A TYR* 2.6 41.2 + - - +
183A VAL* 4.9 1.9 - - - +
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Residues in contact with GLU 145 (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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132A MET* 3.5 41.1 + - - +
141A ALA 3.2 13.7 + - - +
142A VAL* 3.8 5.8 - - - +
143A ALA 3.3 0.2 - - - -
144A GLU* 1.3 79.3 - - - +
146A ALA* 1.3 55.7 + - - +
148A LYS* 2.7 39.0 + - - +
149A GLN* 3.0 70.0 + - - +
657A HIS* 4.5 7.2 - - - +
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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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142A VAL 3.2 13.6 + - - +
143A ALA 3.3 8.3 + - - +
145A GLU* 1.3 75.9 - - - +
147A TYR* 1.3 60.9 + - - +
150A MET* 3.2 24.1 + - - +
157A GLN* 3.4 10.6 - - + +
159A ILE* 4.3 5.2 - - + -
180A PHE* 4.0 16.2 - - + -
433A ILE* 4.0 8.9 - - + +
657A HIS* 3.6 34.1 - - + +
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Residues in contact with TYR 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 ALA 3.1 13.0 + - - +
144A GLU* 3.6 19.5 - - - +
146A ALA* 1.3 74.8 - - - +
148A LYS* 1.3 61.9 + - - +
150A MET* 3.4 41.4 - - + +
151A ALA* 3.8 7.6 + - - +
179A TYR* 5.7 0.7 - - + -
180A PHE* 4.1 18.8 - + + -
183A VAL* 3.8 33.0 + - + -
184A SER* 3.3 17.1 - - - -
228A PHE* 4.0 18.8 - + - -
232A TYR* 3.1 32.7 + + + +
433A ILE* 4.0 6.0 - - + +
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY* 5.3 4.7 - - - +
130A GLN 2.7 29.4 + - - +
131A ASN* 4.0 12.1 - - - +
132A MET 4.3 0.4 - - - +
144A GLU* 2.9 37.2 + - - +
145A GLU* 2.7 42.0 + - - +
147A TYR* 1.3 75.0 - - - +
149A GLN* 1.3 60.6 + - + +
150A MET 3.4 0.2 + - - -
151A ALA* 3.6 4.1 + - - +
152A ARG* 3.1 32.6 + - + +
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Residues in contact with GLN 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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145A GLU* 3.0 50.6 + - - +
146A ALA* 5.0 0.2 - - - -
148A LYS* 1.3 73.2 - - + +
150A MET* 1.3 63.8 + - - +
152A ARG* 3.9 22.6 - - - +
153A ASP* 2.9 35.6 + - - +
155A ARG 4.4 0.3 - - - +
157A GLN* 3.1 20.1 + - - +
655A THR* 5.0 9.3 - - - +
657A HIS* 3.5 20.3 + - - -
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Residues in contact with MET 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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146A ALA 3.2 12.4 + - - +
147A TYR* 3.4 37.9 - - + +
148A LYS 3.2 0.2 - - - -
149A GLN* 1.3 75.2 - - - +
151A ALA* 1.4 55.7 + - + +
154A GLU* 3.0 26.7 + - - +
155A ARG 3.1 28.4 + - - +
157A GLN* 3.2 5.8 - - + +
228A PHE* 4.0 13.2 - - + -
232A TYR* 3.4 42.0 - - + +
431A SER* 4.1 8.1 - - - -
432A PHE 4.1 7.6 - - - +
433A ILE* 3.6 28.3 - - + -
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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 TYR 3.8 6.0 + - - +
148A LYS* 3.6 6.3 + - - +
150A MET* 1.4 76.8 - - - +
152A ARG* 1.3 64.6 + - - +
153A ASP 3.4 0.8 + - - -
154A GLU* 4.0 11.4 + - - +
232A TYR* 4.3 26.2 - - + -
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Residues in contact with ARG 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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148A LYS* 3.1 23.2 + - + +
149A GLN* 4.0 23.7 - - - +
151A ALA* 1.3 78.3 - - - +
153A ASP* 1.4 95.1 + - - +
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Residues in contact with ASP 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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149A GLN* 2.9 25.3 + - - +
152A ARG* 1.4 126.4 + - - +
154A GLU* 1.4 65.8 + - - +
155A ARG* 3.8 23.2 - - + +
157A GLN* 5.6 0.9 - - - -
655A THR* 5.9 0.9 - - - -
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Residues in contact with GLU 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 MET 3.0 10.1 + - - +
151A ALA* 4.0 8.7 + - - +
152A ARG 3.8 1.6 - - - -
153A ASP* 1.4 77.9 - - - +
155A ARG* 1.3 58.2 + - - +
156A ASN* 5.5 1.0 + - - -
232A TYR* 2.7 31.4 + - - -
430A HIS* 2.8 31.1 + - - -
431A SER* 4.6 5.5 + - - -
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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