Contacts of the helix formed by residues 168 - 175 (chain B) in PDB entry 4K9N
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 ASP 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A TYR* 4.7 11.3 + - - -
7B THR* 5.3 0.3 + - - +
133B ALA* 4.3 22.0 + - + +
166B ASP 4.0 0.4 + - - -
167B ALA* 1.3 76.7 - - - +
169B PRO* 1.3 75.5 - - - +
170B GLN* 2.9 30.0 + - - +
171B SER* 3.0 33.2 + - - +
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Residues in contact with PRO 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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167B ALA 3.5 8.7 - - - +
168B ASP* 1.3 89.8 - - - +
170B GLN* 1.3 60.8 + - + +
171B SER 3.0 4.4 + - - -
172B HIS* 3.2 25.3 + - - +
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Residues in contact with GLN 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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286A GLY 3.8 18.4 - - - +
287A GLN* 3.3 27.4 - - + +
288A TYR* 2.9 44.7 + - + +
289A LEU 5.0 0.4 + - - -
309A PRO 4.8 0.9 - - - +
168B ASP* 2.9 18.1 + - - +
169B PRO* 1.3 77.7 - - + +
171B SER* 1.3 59.3 + - - +
172B HIS* 3.1 23.8 + - - -
173B HIS* 2.9 41.4 + - - +
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Residues in contact with SER 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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288A TYR* 5.9 0.4 - - - -
7B THR* 3.8 22.4 - - - -
133B ALA 4.5 3.8 + - - -
136B PRO* 4.1 13.7 - - - +
137B HIS* 5.0 2.1 + - - +
168B ASP* 3.0 30.8 + - - +
170B GLN* 1.3 72.6 - - - +
172B HIS* 1.3 64.8 + - - +
173B HIS 3.0 2.9 - - - -
174B LEU* 2.9 37.8 + - - +
175B PHE* 4.1 7.7 - - - -
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Residues in contact with HIS 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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14B ARG* 5.2 0.9 + - - -
169B PRO 3.2 22.2 + - - +
170B GLN* 3.1 14.8 - - - -
171B SER* 1.3 78.5 - - - +
173B HIS* 1.3 99.5 + + - +
174B LEU 3.0 0.9 + - - -
175B PHE* 3.2 43.9 + - + +
176B ASP 4.7 0.7 + - - -
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Residues in contact with HIS 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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288A TYR* 4.2 8.1 - - + -
289A LEU* 3.6 38.9 + - + +
290A LYS 5.6 1.3 - - - -
291A PRO* 6.4 0.4 - - + -
293A THR 5.9 0.7 - - - -
309A PRO 3.3 20.0 - - - +
310A MET* 3.7 19.0 - - + +
311A GLY 4.5 1.4 + - - -
170B GLN* 2.9 47.0 + - - +
171B SER 3.0 0.6 - - - -
172B HIS* 1.3 105.5 + + - +
174B LEU* 1.3 59.5 + - - +
175B PHE 3.5 0.3 + - - -
176B ASP 4.4 3.2 + - - -
177B ARG* 3.5 15.8 + - - +
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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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308A ALA 4.4 2.0 - - - +
309A PRO* 3.5 25.6 - - + +
7B THR* 5.8 0.2 - - + -
11B LEU* 3.5 22.2 - - + +
15B GLN* 3.8 3.5 + - - -
136B PRO* 3.5 35.0 - - + +
137B HIS* 3.6 31.0 - - + +
140B SER* 3.8 21.7 + - - +
144B HIS* 5.2 0.3 + - - -
171B SER* 2.9 27.8 + - - +
173B HIS* 1.3 78.4 - - - +
175B PHE* 1.3 68.0 + - + +
176B ASP 3.2 0.7 + - - -
177B ARG* 3.5 17.2 + - - +
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Residues in contact with PHE 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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7B THR* 3.5 42.0 - - + -
10B GLU* 3.6 21.1 - - + -
11B LEU* 3.7 26.7 - - + -
14B ARG* 3.4 58.7 - - + +
15B GLN* 2.9 20.1 + - - +
171B SER 4.1 6.7 - - - -
172B HIS* 3.2 38.5 + - + +
174B LEU* 1.3 77.5 - - + +
176B ASP* 1.3 59.4 + - - +
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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