Contacts of the helix formed by residues 129 - 145 (chain A) in PDB entry 3A3K
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PRO* 3.6 15.3 - - - -
125A ARG* 3.7 30.9 + - - -
127A GLY 3.8 1.1 + - - -
128A PRO* 1.3 77.5 - - - +
130A HIS* 1.3 68.9 + - - +
131A VAL* 4.0 11.2 - - - +
132A LYS* 3.2 38.6 + - - +
133A LEU* 3.9 2.3 + - - +
282A TYR* 5.4 1.1 + - - -
371A ASP* 4.2 7.3 - - - +
372A ARG 4.7 1.4 + - - -
374A THR* 3.9 4.1 + - - -
376A PHE* 5.1 2.8 - - - -
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 2.9 54.2 + - + +
111A ALA* 4.2 1.6 - - - -
112A LEU 5.2 0.9 - - - +
129A SER* 1.3 70.0 - - - +
131A VAL* 1.3 64.2 + - - +
132A LYS 3.1 1.8 - - - -
133A LEU* 3.1 24.5 + - + +
134A GLY 3.4 3.6 + - - -
163A PRO* 4.4 3.2 + - - +
166A PHE* 3.3 42.7 - - + +
167A ILE* 3.4 36.0 + - + +
170A GLY* 3.9 17.5 - - - -
171A LEU 4.0 0.3 + - - -
243A VAL* 5.3 3.0 - - + +
282A TYR* 3.9 18.5 + - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO 4.8 0.4 + - - -
112A LEU* 3.7 35.6 - - + +
125A ARG* 5.0 7.9 - - - +
129A SER* 4.0 16.6 - - - +
130A HIS* 1.3 76.3 - - - +
132A LYS* 1.3 66.9 + - + +
134A GLY* 2.8 18.0 + - - -
135A ASP* 3.0 10.2 + - - -
170A GLY* 4.1 17.2 - - - +
174A ARG* 3.4 46.8 - - + +
371A ASP* 5.3 4.0 - - - +
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Residues in contact with LYS 132 (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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129A SER* 3.3 28.7 - - - +
130A HIS 3.1 0.2 - - - -
131A VAL* 1.3 85.0 - - + +
133A LEU* 1.3 59.8 + - - +
135A ASP* 3.1 24.7 + - - +
136A PHE* 3.1 16.6 + - - +
174A ARG* 5.4 2.5 - - - +
367A ASP* 2.8 30.6 + - - +
371A ASP* 3.8 6.0 + - - -
372A ARG 3.3 18.2 - - - +
373A ASP* 2.9 23.3 + - - +
374A THR* 3.5 37.7 - - - +
376A PHE* 3.6 9.1 - - + -
394A TYR* 4.6 2.1 - - - -
396A GLY* 5.9 2.5 - - - +
505A SO4 5.3 1.4 + - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER 3.9 0.4 + - - -
130A HIS* 3.1 17.7 + - - +
132A LYS* 1.3 74.7 - - - +
134A GLY* 1.3 59.8 + - - +
136A PHE* 3.1 10.0 + - + +
137A VAL* 2.9 30.8 + - + +
167A ILE* 3.6 33.4 - - + +
171A LEU* 4.1 17.3 - - + -
241A LEU* 3.7 19.3 - - + -
243A VAL* 4.7 10.1 - - + -
280A ILE* 3.9 22.4 - - + -
376A PHE* 3.6 34.6 - - + -
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Residues in contact with GLY 134 (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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130A HIS 3.4 4.8 + - - -
131A VAL 2.8 9.8 + - - -
133A LEU* 1.3 78.5 - - - +
135A ASP* 1.3 55.8 + - - +
137A VAL* 3.5 0.6 + - - -
138A THR* 2.9 32.9 + - - -
171A LEU* 4.1 8.3 - - - +
174A ARG* 3.7 21.3 - - - -
175A VAL* 3.6 16.4 - - - +
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Residues in contact with ASP 135 (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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131A VAL 3.0 8.8 + - - -
132A LYS* 3.1 30.4 + - + +
134A GLY* 1.3 73.0 - - - +
136A PHE* 1.3 59.9 + - - +
138A THR* 3.4 3.1 - - - -
139A ALA* 3.0 28.2 + - - +
174A ARG* 3.2 33.5 + - - +
178A ARG* 2.8 32.1 + - - +
394A TYR* 3.4 23.9 + - + +
396A GLY 5.2 4.0 - - - +
399A GLN* 4.5 7.7 + - - -
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Residues in contact with PHE 136 (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 LYS 3.1 5.5 + - - +
133A LEU* 3.1 16.4 + - + +
135A ASP* 1.3 77.2 - - - +
137A VAL* 1.3 65.4 + - + +
139A ALA* 3.2 3.1 + - - +
140A LEU* 3.0 36.9 + - + +
280A ILE* 3.6 46.2 - - + -
376A PHE* 3.8 32.8 - - + -
378A LEU* 4.3 25.6 - - + -
392A LEU* 5.8 0.9 - - + -
393A ASN 5.6 0.4 - - - -
394A TYR* 3.4 36.5 - + + -
401A LEU* 3.7 23.1 - - + -
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Residues in contact with VAL 137 (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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133A LEU* 2.9 27.6 + - + +
136A PHE* 1.3 76.2 - - + +
138A THR* 1.3 67.2 + - - +
140A LEU* 3.2 8.0 + - + +
141A HIS* 3.0 39.9 + - + +
171A LEU* 4.0 25.1 - - + -
175A VAL* 3.7 26.7 - - + -
211A TYR* 3.4 38.1 - - + +
241A LEU* 5.4 0.2 - - + -
280A ILE* 5.1 2.2 - - + -
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Residues in contact with THR 138 (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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134A GLY 2.9 24.7 + - - -
135A ASP* 3.4 8.3 - - - -
137A VAL* 1.3 76.7 - - - +
139A ALA* 1.3 62.2 + - - +
141A HIS* 3.4 2.4 + - - +
142A ARG* 3.2 47.4 + - - +
175A VAL* 4.1 12.5 - - - +
178A ARG* 3.8 43.9 - - + +
179A LEU* 3.8 18.9 - - + +
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Residues in contact with ALA 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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135A ASP 3.0 14.6 + - - +
136A PHE 3.5 7.6 - - - +
138A THR* 1.3 75.8 - - - +
140A LEU* 1.3 63.3 + - - +
142A ARG* 3.1 9.9 + - - +
143A ARG* 2.9 23.4 + - - +
394A TYR* 3.7 22.7 - - + -
399A GLN* 4.3 8.3 - - + +
401A LEU* 3.7 17.7 - - + +
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Residues in contact with LEU 140 (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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136A PHE* 3.0 40.2 + - + +
137A VAL* 3.4 10.8 - - - +
139A ALA* 1.3 74.2 - - - +
141A HIS* 1.3 61.7 + - + +
143A ARG* 3.2 2.9 + - - +
144A LEU* 3.0 56.6 + - + +
146A TRP* 4.9 1.3 - - + -
211A TYR* 4.3 10.5 - - - +
239A PHE* 3.9 32.3 - - + -
280A ILE* 4.7 3.1 - - + -
378A LEU* 4.2 10.8 - - + -
392A LEU* 4.2 24.9 - - + -
401A LEU* 3.8 8.4 - - + +
409A LEU* 5.2 0.2 - - + -
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Residues in contact with HIS 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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137A VAL* 3.0 33.1 + - + +
140A LEU* 1.3 78.5 - - + +
142A ARG* 1.3 58.2 + - - +
145A GLY* 3.0 23.6 + - - -
146A TRP* 3.0 64.3 + + + +
149A GLN 4.6 3.1 - - - -
150A ALA* 4.2 9.9 - - + -
179A LEU* 3.5 22.2 - - + +
181A ILE* 4.0 25.5 - - + +
209A VAL* 4.1 10.3 - - + +
211A TYR* 2.7 30.4 + - - -
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Residues in contact with ARG 142 (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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138A THR* 3.2 23.7 + - - +
139A ALA* 3.1 11.0 + - - +
141A HIS* 1.3 76.0 - - - +
143A ARG* 1.3 65.3 - - - +
144A LEU 3.6 0.2 + - - -
145A GLY* 3.8 6.3 + - - -
178A ARG* 3.2 32.7 + - - +
179A LEU* 3.4 18.5 - - + +
504A SO4 2.7 42.4 + - - -
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Residues in contact with ARG 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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139A ALA 2.9 12.1 + - - +
140A LEU* 3.5 9.6 - - - +
142A ARG* 1.3 78.8 - - - +
144A LEU* 1.3 74.2 + - + +
145A GLY 3.8 0.3 + - - -
392A LEU* 4.2 29.8 - - - +
401A LEU* 3.5 46.3 + - + +
403A ALA* 5.0 10.7 - - - +
409A LEU* 5.5 4.0 - - - +
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Residues in contact with LEU 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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140A LEU* 3.0 33.7 + - + +
141A HIS 4.7 0.2 - - - +
143A ARG* 1.3 93.5 - - + +
145A GLY* 1.3 61.9 + - - +
146A TRP* 3.4 52.1 + - + -
239A PHE* 5.2 1.1 - - + -
409A LEU* 4.0 20.9 - - + -
411A TRP* 3.8 21.1 - - + +
416A PRO* 4.0 24.0 - - + +
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Residues in contact with GLY 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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141A HIS 3.0 7.1 + - - -
142A ARG* 3.8 5.6 + - - -
143A ARG 3.5 2.8 - - - -
144A LEU* 1.3 77.9 - - - +
146A TRP* 1.3 63.2 + - - +
147A GLU* 3.4 15.1 + - - +
419A ASP* 5.0 2.3 - - - +
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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