Contacts of the helix formed by residues 129 - 145 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B PRO* 3.7 10.1 - - - -
125B ARG* 3.8 34.5 + - - -
127B GLY 3.6 2.1 + - - -
128B PRO* 1.3 76.9 - - - +
130B HIS* 1.3 68.2 + - - +
131B VAL* 4.1 10.0 - - - +
132B LYS* 3.3 39.0 + - - +
133B LEU* 3.8 2.8 + - - +
282B TYR* 5.3 0.7 + - - -
371B ASP* 4.2 7.6 - - - +
372B ARG 4.6 1.2 + - - -
374B THR* 3.7 5.5 + - - -
376B PHE* 5.0 3.3 - - - -
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Residues in contact with HIS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 2.9 54.0 + - + +
111B ALA* 4.3 1.3 - - - -
112B LEU 5.3 0.7 - - - +
129B SER* 1.3 71.5 - - - +
131B VAL* 1.3 64.4 + - - +
132B LYS 3.2 1.6 - - - -
133B LEU* 3.1 24.9 + - + +
134B GLY 3.4 4.0 + - - -
163B PRO* 4.4 2.6 + - - +
166B PHE* 3.5 41.1 - - + +
167B ILE* 3.4 35.9 + - + +
170B GLY* 3.7 16.5 - - - -
171B LEU 3.8 0.7 + - - -
243B VAL* 5.5 3.4 - - + +
282B TYR* 3.9 19.2 + - - -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO 4.8 0.8 + - - -
112B LEU* 3.8 34.3 - - + -
115B GLY* 6.5 0.2 - - - -
125B ARG* 5.3 6.7 - - - +
129B SER* 4.1 14.1 - - - +
130B HIS* 1.3 73.4 - - - +
132B LYS* 1.3 71.2 + - + +
134B GLY* 2.9 17.3 + - - -
135B ASP 3.0 9.2 + - - -
170B GLY* 4.0 19.7 - - - +
174B ARG* 3.5 46.6 + - + +
371B ASP* 5.4 3.4 - - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 3.4 28.5 - - - +
131B VAL* 1.3 85.5 - - + +
133B LEU* 1.3 60.0 + - - +
135B ASP* 3.1 31.1 + - + +
136B PHE 3.2 9.4 + - - -
174B ARG* 5.2 1.7 - - - +
367B ASP* 2.5 32.0 + - - +
371B ASP* 4.1 5.2 - - - -
372B ARG 3.4 16.6 - - - +
373B ASP* 2.9 25.0 + - - +
374B THR* 3.7 31.9 - - - +
376B PHE* 3.6 10.0 - - + -
394B TYR* 4.5 2.3 - - + -
396B GLY* 5.6 3.6 + - - +
506B SO4 5.2 1.8 + - - -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER 3.8 1.0 + - - +
130B HIS* 3.1 19.1 + - - +
132B LYS* 1.3 73.6 - - - +
134B GLY* 1.3 60.2 + - - +
136B PHE* 3.1 9.4 + - + +
137B VAL* 3.0 29.7 + - + +
167B ILE* 3.7 33.2 - - + +
171B LEU* 3.7 27.6 - - + -
241B LEU* 4.3 12.3 - - + -
243B VAL* 4.9 9.0 - - + -
280B ILE* 4.1 21.3 - - + -
282B TYR* 6.1 0.2 - - + -
376B PHE* 3.5 35.8 - - + -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B HIS 3.4 4.8 + - - -
131B VAL 2.9 10.0 + - - -
133B LEU* 1.3 80.2 - - - +
135B ASP* 1.3 53.4 + - - +
137B VAL* 4.6 0.9 - - - -
138B THR* 2.7 33.4 + - - -
171B LEU* 4.1 10.4 - - - +
174B ARG* 3.7 17.5 - - - -
175B VAL* 3.4 18.5 - - - +
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL 3.0 7.7 + - - -
132B LYS* 3.1 29.0 + - - +
134B GLY* 1.3 74.3 - - - +
136B PHE* 1.3 65.3 + - - +
138B THR* 3.3 5.1 + - - -
139B ALA* 3.0 22.5 + - - +
174B ARG* 2.9 37.7 + - - -
178B ARG* 2.8 33.7 + - - +
394B TYR* 3.4 20.6 + - + +
396B GLY 5.5 3.0 - - - +
399B GLN* 4.5 7.1 + - - +
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS 3.2 2.4 + - - +
133B LEU* 3.1 14.9 + - + +
135B ASP* 1.3 78.4 - - - +
137B VAL* 1.3 67.6 + - + +
139B ALA* 3.1 5.7 + - - +
140B LEU* 3.0 39.8 + - + +
280B ILE* 3.5 47.8 - - + -
376B PHE* 3.8 30.7 - - + -
377B SER 4.8 1.6 - - - -
378B LEU* 4.3 23.3 - - + -
392B LEU 5.8 0.9 - - - -
393B ASN 5.7 0.2 - - - -
394B TYR* 3.4 45.4 - + + -
401B LEU* 3.8 16.2 - - + -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.0 19.8 + - + +
136B PHE* 1.3 83.8 - - + +
138B THR* 1.3 62.6 + - - +
140B LEU* 3.0 8.3 + - - +
141B HIS* 2.9 40.3 + - + +
171B LEU* 4.0 28.0 - - + -
175B VAL* 3.8 24.0 - - + -
211B TYR* 3.3 39.0 - - + +
241B LEU* 5.4 0.2 - - + -
280B ILE* 5.2 2.2 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY 2.7 19.3 + - - -
135B ASP* 3.3 11.9 - - - -
137B VAL* 1.3 76.0 - - - +
139B ALA* 1.3 62.0 + - - +
141B HIS* 3.3 2.8 + - - +
142B ARG* 3.1 57.7 + - - +
175B VAL* 3.9 11.3 - - - +
178B ARG* 4.0 30.8 - - + +
179B LEU* 3.8 22.9 - - + +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP 3.0 12.7 + - - +
136B PHE 3.1 8.3 + - - +
138B THR* 1.3 76.5 - - - +
140B LEU* 1.3 57.8 + - - +
142B ARG* 3.7 8.0 + - - +
143B ARG* 3.2 20.6 + - - +
394B TYR* 3.9 23.6 - - + -
399B GLN* 4.4 11.4 - - - +
401B LEU* 3.4 24.1 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PHE* 3.0 45.7 + - + +
137B VAL* 3.0 10.0 + - - +
139B ALA* 1.3 76.5 - - - +
141B HIS* 1.3 69.7 + - + +
143B ARG* 3.5 1.9 + - - +
144B LEU* 3.1 56.0 + - + +
146B TRP* 4.8 0.9 - - + -
211B TYR* 4.4 9.6 - - - +
239B PHE* 4.1 26.9 - - + -
280B ILE* 4.5 4.0 - - + -
378B LEU* 4.4 18.8 - - + -
392B LEU* 4.4 15.5 - - + -
401B LEU* 4.3 5.4 - - + -
409B LEU* 5.1 1.6 - - + -
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Residues in contact with HIS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B VAL* 2.9 29.0 + - + +
138B THR 3.3 0.4 + - - +
140B LEU* 1.3 78.0 - - + +
142B ARG* 1.3 57.3 + - - +
145B GLY* 2.8 26.5 + - - -
146B TRP* 2.9 61.8 + + + +
149B GLN 4.7 2.7 + - - -
150B ALA* 4.1 17.3 - - + -
179B LEU* 3.6 20.6 - - + -
181B ILE* 3.9 26.9 - - + +
209B VAL* 4.2 4.3 - - + -
211B TYR* 2.7 32.6 + + - -
419B ASP* 5.2 0.2 + - - -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 3.1 31.3 + - - +
139B ALA* 4.0 7.2 - - - +
141B HIS* 1.3 78.2 - - - +
143B ARG* 1.3 61.4 + - - +
144B LEU 3.2 0.7 + - - -
145B GLY* 3.5 7.4 + - - -
178B ARG* 3.3 29.3 + - - +
179B LEU* 3.6 16.6 - - + +
507B SO4 2.8 47.2 + - - -
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ALA 3.2 16.2 + - - +
140B LEU* 3.9 5.4 - - - +
141B HIS 3.4 0.2 - - - -
142B ARG* 1.3 78.3 - - - +
144B LEU* 1.3 73.4 - - + +
392B LEU* 4.1 33.0 - - - +
401B LEU* 3.8 39.1 + - + +
403B ALA* 5.0 9.1 - - - +
409B LEU* 5.4 6.0 - - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.1 34.4 + - + +
143B ARG* 1.3 93.1 - - + +
145B GLY* 1.3 62.2 + - - +
146B TRP* 3.4 54.8 + - + -
239B PHE* 5.1 1.3 - - + -
409B LEU* 4.1 20.4 - - + -
411B TRP* 4.1 20.4 - - + +
416B PRO* 4.1 22.8 - - + +
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B HIS 2.8 6.4 + - - -
142B ARG 3.5 7.8 + - - -
143B ARG 3.6 0.4 - - - -
144B LEU* 1.3 79.3 - - - +
146B TRP* 1.3 64.9 + - - +
147B GLU* 3.5 21.6 + - - +
148B HIS* 5.7 0.2 + - - -
419B ASP* 4.9 2.6 - - - +
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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
------------------------------------------------------------
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