Contacts of the helix formed by residues 136 - 150 (chain B) in PDB entry 1ND4
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 GLN 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B ASP* 2.6 42.7 + - - +
135B HIS* 1.3 81.0 - - - +
137B ALA* 1.3 67.4 + - - +
138B LYS* 3.9 19.9 - - + +
139B HIS* 3.2 22.2 + - + +
140B ARG* 3.0 17.7 + - - +
182B GLU* 3.6 18.5 - - - +
184B LEU* 5.0 15.7 - - + -
214B VAL 3.6 2.4 + - - +
215B ALA* 5.2 1.1 - - - +
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Residues in contact with ALA 137 (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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135B HIS 3.7 0.8 + - - -
136B GLN* 1.3 72.7 - - - +
138B LYS* 1.3 58.2 + - - +
140B ARG* 3.7 5.1 - - - +
141B ILE* 2.8 35.9 + - - +
178B MET* 3.8 21.3 - - - -
179B PRO* 4.4 13.5 - - + +
182B GLU* 2.8 27.6 + - + +
215B ALA* 5.8 0.2 - - - +
256B PHE* 4.4 12.3 - - + -
257B TYR* 4.7 7.6 - - - +
260B LEU* 5.6 1.1 - - - +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLN* 3.9 23.3 - - + +
137B ALA* 1.3 78.0 - - - +
139B HIS* 1.3 95.0 + - + +
141B ILE* 3.3 3.7 + - - +
142B GLU* 3.1 23.4 + - - +
178B MET* 4.0 22.9 - - + +
182B GLU* 5.3 1.7 + - - +
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Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP* 2.9 48.5 + - - +
136B GLN* 3.2 27.5 + - + +
138B LYS* 1.3 96.5 - - + +
140B ARG* 1.3 62.2 + - + +
142B GLU* 3.3 9.0 + - - +
143B ARG* 2.9 27.6 + - - +
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Residues in contact with ARG 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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59B GLU* 4.8 1.2 + - - -
134B ASP 5.4 0.2 - - - -
135B HIS* 3.4 53.2 + - + +
136B GLN 3.0 16.9 + - - +
137B ALA* 3.8 4.7 - - - +
139B HIS* 1.3 75.5 - - - +
141B ILE* 1.3 60.8 + - - +
143B ARG* 3.6 23.3 - - - +
144B ALA* 2.8 29.8 + - - +
189B GLY* 5.6 1.0 + - - -
211B ARG* 3.7 29.9 - - - +
219B GLN* 6.1 1.4 - - - +
260B LEU* 3.9 26.8 - - + +
264B PHE* 3.2 41.7 - - + -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA 2.8 21.2 + - - +
138B LYS* 3.6 4.7 - - - +
140B ARG* 1.3 77.0 - - - +
142B GLU* 1.3 64.5 + - - +
144B ALA* 3.0 11.0 + - - +
145B ARG 2.9 17.2 + - - -
171B PHE* 3.4 14.5 - - + -
174B LEU* 4.3 15.3 - - + +
175B LYS* 3.7 31.2 - - + -
178B MET* 3.6 44.2 - - + -
256B PHE* 3.9 26.5 - - + -
260B LEU* 4.3 4.0 - - + -
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Residues in contact with GLU 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 LYS 3.1 13.6 + - - +
139B HIS* 3.5 11.2 - - - +
141B ILE* 1.3 78.4 - - - +
143B ARG* 1.3 58.3 + - - +
145B ARG* 2.5 52.2 + - - +
146B THR* 2.8 30.4 + - + +
171B PHE* 5.3 0.2 - - - -
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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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56B ALA* 3.3 27.1 + - - +
57B LEU* 3.1 22.2 - - - +
59B GLU* 6.1 1.0 - - - +
62B ASP* 4.3 12.9 + - - -
139B HIS 2.9 17.6 + - - +
140B ARG* 3.6 27.9 - - - +
142B GLU* 1.3 73.9 - - - +
144B ALA* 1.3 66.8 + - - +
146B THR* 2.6 36.3 + - - -
147B ARG* 2.9 22.4 + - + +
264B PHE* 4.4 9.6 - - + -
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Residues in contact with ALA 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 ARG 2.8 13.8 + - - +
141B ILE 3.2 12.3 - - - +
143B ARG* 1.3 76.8 - - - +
145B ARG* 1.3 55.7 + - - +
147B ARG* 3.5 5.5 + - - +
148B MET* 3.0 27.7 + - - +
171B PHE* 4.5 0.9 - - + -
174B LEU* 4.2 7.0 - - + -
260B LEU* 3.9 16.4 - - + -
263B PHE* 3.6 38.5 - - + -
264B PHE* 4.3 5.8 - - + -
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Residues in contact with ARG 145 (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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141B ILE 2.9 5.3 + - - +
142B GLU* 2.5 50.0 + - - +
144B ALA* 1.3 75.5 - - - +
146B THR* 1.3 80.8 + - - +
148B MET* 3.0 13.0 + - + +
149B GLU* 2.8 61.9 + - - +
171B PHE* 3.5 38.8 - - + -
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Residues in contact with THR 146 (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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57B LEU* 4.3 11.0 - - - +
142B GLU* 2.8 26.9 + - + +
143B ARG* 2.6 37.4 + - - -
145B ARG* 1.3 94.3 - - - +
147B ARG* 1.3 57.1 + - - +
149B GLU* 3.3 9.3 + - - +
150B ALA* 3.0 28.5 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.6 20.1 + - + +
59B GLU* 5.1 9.7 + - - -
143B ARG* 2.9 35.4 + - + +
144B ALA* 3.7 5.4 - - - +
146B THR* 1.3 76.4 + - - +
148B MET* 1.3 63.2 + - - +
150B ALA* 3.3 1.7 + - - -
151B GLY 3.2 3.3 + - - -
152B LEU* 2.8 81.4 + - + +
153B VAL* 4.8 1.1 - - - -
211B ARG* 5.3 1.2 - - - +
263B PHE 2.6 35.3 + - - +
264B PHE* 3.7 44.6 + - - +
2300B KAN 6.1 0.2 + - - -
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Residues in contact with MET 148 (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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144B ALA 3.0 14.4 + - - +
145B ARG* 3.0 17.7 + - + +
147B ARG* 1.3 74.1 - - - +
149B GLU* 1.3 62.8 + - + +
151B GLY* 2.7 24.1 + - - -
153B VAL* 4.0 10.9 - - + +
167B PRO* 3.6 46.7 - - + +
168B ALA* 3.7 9.0 - - + -
171B PHE* 3.7 35.9 - - + -
263B PHE* 4.1 10.3 - - + -
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 2.8 65.4 + - + +
146B THR* 3.6 10.1 - - - +
148B MET* 1.3 83.4 - - + +
150B ALA* 1.3 57.2 + - - +
151B GLY* 3.2 3.5 + - - -
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Residues in contact with ALA 150 (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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57B LEU* 4.1 11.0 - - + -
146B THR 3.0 16.9 + - - +
147B ARG 3.6 6.3 - - - +
148B MET 3.1 0.4 - - - -
149B GLU* 1.3 76.4 - - - +
151B GLY* 1.3 62.3 + - - +
152B LEU* 3.2 26.7 + - + +
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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