Contacts of the helix formed by residues 166 - 177 (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 ALA 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B GLN* 4.4 3.8 - - - +
164B GLY 3.7 2.8 + - - -
165B LEU* 1.3 70.9 - - - +
167B PRO* 1.3 64.7 - - + +
168B ALA* 4.4 7.9 - - + +
169B GLU* 2.7 36.0 + - + +
170B LEU* 3.0 11.1 - - - +
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Residues in contact with PRO 167 (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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148B MET* 3.6 26.4 - - + +
153B VAL* 4.2 23.6 - - + -
155B GLN* 3.7 37.7 - - + +
165B LEU 3.7 1.8 - - - +
166B ALA* 1.3 84.5 - - + +
168B ALA* 1.3 53.1 + - - +
170B LEU* 3.0 13.6 + - + +
171B PHE* 2.7 35.3 + - - +
263B PHE* 3.9 3.4 - - + -
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Residues in contact with ALA 168 (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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148B MET* 3.7 14.4 - - + -
166B ALA* 3.0 6.8 + - + +
167B PRO* 1.3 78.5 - - - +
169B GLU* 1.3 56.3 + - - +
171B PHE* 3.4 4.8 + - - +
172B ALA* 3.0 28.4 + - - +
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Residues in contact with GLU 169 (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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165B LEU* 4.1 22.9 - - + -
166B ALA* 2.7 28.8 + - + +
168B ALA* 1.3 71.5 - - - +
170B LEU* 1.3 61.4 + - - +
172B ALA* 3.3 8.7 + - - +
173B ARG* 2.7 68.2 + - - +
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Residues in contact with LEU 170 (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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158B LEU* 5.0 13.7 - - + -
162B HIS* 3.8 38.6 - - + +
165B LEU* 3.4 42.0 - - + +
166B ALA 3.0 27.1 - - - +
167B PRO* 3.0 10.4 + - + +
169B GLU* 1.3 72.1 - - - +
171B PHE* 1.3 61.9 + - - +
173B ARG* 3.4 8.0 + - - +
174B LEU* 2.9 28.6 + - - +
259B LEU* 3.6 18.5 - - + +
262B GLU* 5.3 2.5 - - + -
263B PHE* 3.7 17.5 - - + -
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Residues in contact with PHE 171 (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* 3.4 32.8 - - + -
142B GLU* 5.3 0.2 - - - -
144B ALA 4.8 0.2 - - - -
145B ARG* 3.5 37.2 - - + -
148B MET* 3.7 24.5 - - + -
167B PRO 2.7 19.6 + - - +
168B ALA* 3.6 5.8 - - - +
170B LEU* 1.3 74.9 - - - +
172B ALA* 1.3 57.3 + - - +
174B LEU* 3.2 15.4 + - + +
175B LYS* 2.8 71.4 + - + +
263B PHE* 3.4 14.8 - + + -
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Residues in contact with ALA 172 (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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168B ALA 3.0 14.1 + - - +
169B GLU* 3.5 16.2 - - - +
171B PHE* 1.3 77.6 - - - +
173B ARG* 1.3 63.1 + - + +
175B LYS* 3.3 7.7 + - - +
176B ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 173 (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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161B GLU* 4.4 6.3 + - - -
162B HIS* 4.3 13.1 + - - -
165B LEU* 3.5 38.2 - - - +
169B GLU* 2.7 38.5 + - - +
170B LEU* 3.7 15.5 - - - +
172B ALA* 1.3 75.8 - - + +
174B LEU* 1.3 63.1 + - - +
176B ALA* 3.4 2.1 + - - -
177B ARG* 2.9 57.3 + - - +
259B LEU* 3.7 12.3 - - + -
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Residues in contact with LEU 174 (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* 4.3 11.0 - - + -
144B ALA* 4.2 5.2 - - + -
170B LEU 2.9 14.1 + - - +
171B PHE* 3.3 30.3 - - + +
173B ARG* 1.3 76.9 - - - +
175B LYS* 1.3 64.3 + - - +
177B ARG* 3.1 10.7 + - - -
178B MET 3.4 0.2 + - - -
256B PHE* 3.4 50.6 - - + +
259B LEU* 3.6 11.9 - - + +
260B LEU* 3.7 46.0 - - + +
263B PHE* 3.9 19.7 - - + -
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Residues in contact with LYS 175 (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* 3.7 21.3 - - + -
171B PHE* 2.8 60.5 + - + +
172B ALA* 3.6 7.2 - - - +
174B LEU* 1.3 72.2 - - - +
176B ALA* 1.3 62.8 + - - +
177B ARG 3.1 1.2 + - - -
178B MET* 3.1 20.1 + - - +
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Residues in contact with ALA 176 (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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172B ALA 3.0 16.8 + - - +
173B ARG* 3.7 5.6 - - - +
175B LYS* 1.3 75.7 - - - +
177B ARG* 1.3 70.7 + - + +
178B MET 3.4 2.2 + - - +
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Residues in contact with ARG 177 (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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173B ARG* 2.9 52.5 + - - +
174B LEU* 3.1 6.5 + - - +
176B ALA* 1.3 86.2 - - + +
178B MET* 1.3 67.6 + - - +
179B PRO* 3.1 5.4 - - - +
252B GLN 5.4 1.9 - - - +
255B ALA* 5.3 8.7 - - - +
256B PHE* 3.3 34.7 - - + +
259B LEU* 4.0 16.0 - - - +
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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