Contacts of the helix formed by residues 205 - 213 (chain A) in PDB entry 1P4K
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 HIS 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PRO* 2.9 45.4 + - + -
144A ILE* 4.9 0.2 - - - -
145A VAL* 3.6 24.1 - - + +
173A MET* 5.0 5.8 - - - -
204A GLY* 1.3 66.7 - - - -
206A GLY* 1.3 59.5 + - - +
207A GLU* 3.3 8.1 - - + +
208A GLU* 2.9 41.4 + - + +
209A VAL* 3.5 6.7 + - - +
252A ASP 3.4 22.6 + - - -
253A ILE* 3.8 7.0 - - + -
254A GLN* 2.9 38.2 + - + +
255A VAL* 4.2 1.3 - - - +
297A GOL 5.0 0.2 - - - -
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ARG* 4.3 0.6 - - - +
183A ASP* 3.1 24.5 - - - +
204A GLY 2.8 9.6 + - - -
205A HIS* 1.3 70.5 - - - +
207A GLU* 1.3 64.2 + - - +
209A VAL* 3.0 3.1 + - - -
210A ILE* 2.9 27.3 + - - +
297A GOL 2.7 28.0 + - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 5.4 1.0 + - - -
173A MET* 4.7 4.3 - - - +
180A ARG* 2.9 40.6 + - - +
181A VAL 4.7 3.3 - - - +
205A HIS* 3.1 5.8 + - + +
206A GLY* 1.3 76.4 + - - +
208A GLU* 1.3 63.7 + - + +
210A ILE* 3.6 3.4 + - - +
211A ARG* 3.1 38.5 + - - +
376C ILE* 4.5 2.6 - - - +
400C PRO 3.7 20.6 - - - +
401C HIS* 3.4 18.5 - - - +
402C VAL* 3.8 38.6 + - + +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A HIS* 2.9 18.3 + - + +
207A GLU* 1.3 81.2 - - + +
209A VAL* 1.3 60.5 + - - +
211A ARG* 2.8 49.4 + - - +
212A THR* 2.9 28.4 + - - +
239A ILE* 4.5 9.4 - - + +
242A ILE* 5.7 0.9 - - - +
243A VAL* 4.6 11.6 - - - +
246A ARG* 4.1 9.2 + - - -
253A ILE* 3.8 44.0 - - + +
255A VAL* 4.3 8.3 - - + -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ASP* 3.5 22.9 - - + +
189A ALA* 3.2 33.8 - - - +
202A ALA* 3.9 13.0 - - + -
203A THR 5.2 4.3 - - - +
205A HIS 4.1 6.3 - - - +
206A GLY* 3.0 5.7 + - - +
208A GLU* 1.3 74.9 - - - +
210A ILE* 1.3 61.9 + - - +
212A THR* 3.4 4.8 + - - -
213A VAL* 2.8 26.0 + - - -
214A GLY* 3.1 19.1 + - - +
239A ILE* 5.7 0.7 - - + -
255A VAL* 3.9 35.2 - - + -
257A PHE* 4.4 1.3 - - + -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL 4.1 6.5 - - - +
182A GLY* 3.5 27.8 - - - +
183A ASP* 3.8 13.7 - - + +
186A ILE* 3.5 22.7 - - + -
189A ALA* 4.1 9.8 - - + +
206A GLY 2.9 15.9 + - - +
207A GLU* 3.7 7.9 - - - +
209A VAL* 1.3 77.5 - - - +
211A ARG* 1.3 63.8 + - - +
212A THR 3.2 1.0 + - - -
213A VAL* 3.2 17.2 + - - +
376C ILE* 3.7 17.9 - - + -
402C VAL* 3.7 20.9 - - + -
403C MET* 5.1 2.9 - - + -
487C ILE* 3.8 25.0 - - + +
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU* 3.1 15.7 + - - +
208A GLU* 2.8 48.3 + - - +
209A VAL 3.4 0.2 - - - -
210A ILE* 1.3 79.4 - - - +
212A THR* 1.3 68.8 + - + +
242A ILE* 4.4 4.7 - - - -
246A ARG* 3.4 42.7 - - - +
370C MET* 5.4 0.7 - - - +
374C TYR* 2.8 68.5 + - + +
375C ASN* 4.0 3.0 - - - +
376C ILE* 3.7 31.0 - - + +
402C VAL* 4.1 16.3 - - - +
487C ILE* 4.7 3.1 - - - +
492C PHE* 3.8 9.2 - - - -
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU* 2.9 19.0 + - + +
209A VAL* 3.4 7.4 + - - -
210A ILE 3.1 0.2 - - - -
211A ARG* 1.3 86.0 - - + +
213A VAL* 1.3 75.6 + - - +
214A GLY* 3.2 6.7 + - - -
217A LEU* 4.4 4.6 - - - +
238A ARG* 4.1 10.3 + - - +
239A ILE* 3.4 37.5 - - + +
242A ILE* 3.5 33.2 - - + -
257A PHE* 5.1 0.2 - - - -
374C TYR* 4.5 4.3 - - - -
492C PHE* 4.9 0.7 - - - -
516C HIS* 3.9 10.7 - - - -
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE 5.4 0.4 - - - +
188A GLY 3.2 22.8 - - - +
189A ALA* 4.6 2.5 - - + +
209A VAL 2.8 8.0 + - - -
210A ILE* 3.2 12.4 + - - +
212A THR* 1.3 82.4 - - - +
214A GLY* 1.3 64.2 + - - +
216A HIS* 3.8 2.0 - - + -
217A LEU* 3.2 15.2 + - - +
487C ILE* 4.3 4.7 - - + +
488C GLY* 3.9 12.1 - - - -
492C PHE* 3.5 32.8 - - + -
513C VAL* 3.5 29.6 - - + -
516C HIS* 3.6 18.6 - - + +
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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
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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