Contacts of the helix formed by residues 176 - 183 (chain B) in PDB entry 3DDN
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B TYR 3.8 1.6 + - - -
175B VAL* 1.3 75.2 - - - +
177B PRO* 1.3 68.5 - - - +
178B ALA* 3.6 6.1 + - - +
179B ARG* 3.4 26.6 + - - +
180B ALA* 2.9 22.0 + - - +
206B LYS* 5.8 1.2 - - - +
356B GLU* 3.8 22.8 - - - +
359B ALA* 4.1 24.7 - - - +
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Residues in contact with PRO 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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175B VAL 3.2 9.9 - - - +
176B SER* 1.3 82.9 - - - +
178B ALA* 1.3 56.6 + - - +
180B ALA* 3.3 3.3 + - - +
181B ALA* 3.0 28.2 + - - +
187B LEU* 4.0 20.4 - - + -
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Residues in contact with ALA 178 (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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176B SER* 3.2 8.1 + - - +
177B PRO* 1.3 78.1 - - - +
179B ARG* 1.3 64.7 + - - +
181B ALA* 3.4 6.2 + - - +
182B GLN* 3.0 26.9 + - + +
355B GLY 6.2 0.7 - - - -
356B GLU* 3.9 16.8 - - + +
404B SER 6.0 1.8 - - - +
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Residues in contact with ARG 179 (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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152B ARG* 3.5 11.8 - - - +
155B GLN* 2.9 38.1 - - - +
175B VAL* 4.3 9.0 - - + -
176B SER* 3.0 25.7 + - - +
178B ALA* 1.3 77.6 - - - +
180B ALA* 1.3 65.8 + - - +
182B GLN* 3.1 5.6 + - - +
183B LEU* 3.0 40.9 + - + +
323B GLU* 3.3 34.0 + - - -
356B GLU* 3.0 39.4 + - + +
410B ARG* 3.8 10.6 - - - +
411B SER* 5.5 1.0 + - - -
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Residues in contact with ALA 180 (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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150B LEU* 4.9 2.0 - - + -
175B VAL* 4.6 5.8 - - + +
176B SER 2.9 12.7 + - - +
177B PRO 3.4 9.0 - - - +
179B ARG* 1.3 76.4 - - - +
181B ALA* 1.3 57.8 + - - +
183B LEU* 2.9 28.3 + - - +
184B GLY 3.2 0.2 + - - -
185B ILE* 3.0 30.3 + - + +
187B LEU* 3.7 35.4 - - + -
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Residues in contact with ALA 181 (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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177B PRO 3.0 16.2 + - - +
178B ALA* 3.9 6.7 - - - +
180B ALA* 1.3 75.4 - - - +
182B GLN* 1.3 62.7 + - + +
184B GLY* 3.0 13.7 + - - -
185B ILE 4.1 10.0 + - - +
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Residues in contact with GLN 182 (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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159B GLN* 4.8 5.2 + - - -
178B ALA* 3.0 18.2 + - + +
179B ARG 3.1 8.5 + - - +
181B ALA* 1.3 75.8 - - + +
183B LEU* 1.3 62.4 + - + +
184B GLY 3.2 1.0 + - - -
356B GLU* 3.6 3.1 - - - +
410B ARG* 3.4 55.3 + - - +
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Residues in contact with LEU 183 (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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150B LEU* 5.1 2.2 - - + -
152B ARG* 4.2 15.5 - - - +
155B GLN* 3.6 40.2 - - + +
158B ALA 4.9 3.3 - - - +
159B GLN* 3.6 51.6 + - + +
162B ALA* 5.1 5.7 - - - +
168B VAL* 5.9 0.7 - - - +
175B VAL* 5.7 0.4 - - + -
179B ARG* 3.0 31.9 + - + +
180B ALA* 2.9 10.3 + - - +
182B GLN* 1.3 78.3 - - + +
184B GLY* 1.3 59.7 + - - +
185B ILE* 3.7 25.8 + - + +
410B ARG* 6.3 0.2 - - - +
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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