Contacts of the helix formed by residues 210 - 219 (chain A) in PDB entry 3P4P
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 GLY 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A THR* 5.9 1.9 + - - -
193A GLY 5.4 2.0 - - - -
194A GLY 3.5 17.9 + - - -
195A ALA* 4.1 12.8 - - - +
209A THR* 1.3 77.1 - - - +
211A ASP* 1.3 66.4 + - - +
212A GLY 3.0 4.5 + - - -
213A MET* 3.1 10.4 + - - +
214A GLY* 2.9 20.8 + - - -
510A HIS* 3.9 4.5 - - - +
514A VAL* 4.0 7.2 - - - +
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Residues in contact with ASP 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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37A LYS* 2.9 28.3 + - - +
156A PHE* 3.3 24.0 - - + -
192A THR* 5.7 4.8 - - + -
209A THR* 3.2 10.3 + - - -
210A GLY* 1.3 76.9 - - - +
212A GLY* 1.3 62.0 + - - +
214A GLY* 3.3 1.6 + - - -
215A MET* 3.1 39.0 + - + +
507A GLU* 3.2 30.3 - - - +
510A HIS* 3.5 21.5 + - + +
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Residues in contact with GLY 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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190A MET* 3.9 18.5 - - - +
192A THR* 3.2 35.8 + - - -
210A GLY 3.1 1.0 - - - -
211A ASP* 1.3 81.0 - - - +
213A MET* 1.3 60.6 + - - +
215A MET* 3.4 16.1 + - - +
216A ALA* 3.4 11.3 + - - +
361A ILE* 4.1 5.8 - - - +
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Residues in contact with MET 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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192A THR* 4.3 1.6 + - - -
193A GLY 4.3 0.4 - - - +
194A GLY* 4.2 9.0 - - - -
195A ALA* 4.1 15.9 - - - -
210A GLY* 3.1 11.4 + - - +
212A GLY* 1.3 72.8 - - - +
214A GLY* 1.4 65.8 + - - +
216A ALA* 3.3 5.4 + - - +
217A LEU* 3.1 19.1 + - - +
223A LEU* 3.6 29.1 - - + +
226A MET* 3.7 21.8 - - + -
357A THR* 3.6 22.2 - - + -
359A GLY 3.6 7.6 - - - +
360A GLY* 3.6 3.6 - - - -
361A ILE* 4.2 5.1 - - - +
379A GLU 3.5 25.4 - - - +
380A CYS* 3.5 26.9 - - + +
514A VAL* 4.1 7.4 - - + -
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Residues in contact with GLY 214 (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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210A GLY 2.9 12.4 + - - -
211A ASP 3.3 0.2 + - - -
213A MET* 1.4 73.9 - - - +
215A MET* 1.3 64.4 + - - +
217A LEU* 3.0 12.9 + - - +
218A SER* 3.0 22.1 + - - -
510A HIS* 3.6 26.5 - - - -
513A ASN* 5.1 7.1 + - - -
514A VAL* 4.1 10.4 - - - +
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Residues in contact with MET 215 (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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10A VAL* 5.2 1.6 - - + -
157A VAL* 2.8 54.7 - - + +
158A LEU 3.9 17.5 - - - +
159A ASP* 4.1 17.3 - - - +
160A ILE* 4.6 9.2 - - + -
190A MET* 4.3 21.3 - - + +
192A THR* 5.8 1.1 - - + -
211A ASP* 3.1 31.0 + - + +
212A GLY* 3.6 9.9 - - - +
213A MET 3.3 0.2 - - - -
214A GLY* 1.3 74.0 - - - +
216A ALA* 1.3 63.1 + - - +
218A SER* 3.2 11.0 - - - -
219A HIS* 3.0 26.6 - - - -
510A HIS* 4.1 10.2 - - + +
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Residues in contact with ALA 216 (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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160A ILE* 5.2 6.1 - - - -
190A MET* 5.7 1.7 - - + -
212A GLY 3.4 2.9 + - - +
213A MET 3.3 9.3 + - - +
214A GLY 3.1 0.4 - - - -
215A MET* 1.3 79.7 - - - +
217A LEU* 1.3 63.1 + - - +
219A HIS* 3.1 12.8 + - - -
221A VAL* 3.2 39.6 + - + +
223A LEU* 4.6 2.2 - - + -
361A ILE* 3.9 32.8 - - + -
374A LEU* 5.2 5.8 - - + -
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Residues in contact with LEU 217 (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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213A MET 3.1 10.2 + - - +
214A GLY* 3.0 12.0 + - - +
216A ALA* 1.3 75.7 - - - +
218A SER* 1.3 64.0 + - - +
219A HIS 2.9 1.2 + - - -
220A GLY* 3.0 12.1 + - - -
221A VAL 3.7 12.9 + - - +
223A LEU* 3.7 25.8 - - + +
513A ASN* 3.9 29.4 - - + +
514A VAL* 4.6 1.3 - - - +
517A CYS* 3.6 24.2 - - - -
553A ALA 3.5 24.7 - - - +
555A ARG* 3.7 46.3 + - + +
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Residues in contact with SER 218 (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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159A ASP* 4.6 9.1 + - - -
214A GLY 3.0 13.1 + - - -
215A MET* 3.2 18.1 - - - -
217A LEU* 1.3 75.5 - - - +
219A HIS* 1.3 69.5 + - - +
220A GLY 3.7 0.5 + - - -
510A HIS* 5.6 3.3 - - - -
513A ASN* 5.6 3.5 + - - +
555A ARG* 5.5 1.4 - - - +
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Residues in contact with HIS 219 (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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159A ASP* 2.7 29.4 + - - -
160A ILE* 3.4 36.3 - - + +
162A VAL* 3.7 18.8 - - + +
215A MET 3.0 25.1 - - - +
216A ALA 3.1 6.0 + - - +
217A LEU 2.9 1.2 + - - -
218A SER* 1.3 85.7 + - - +
220A GLY* 1.3 62.2 + - - +
221A VAL* 3.3 2.9 + - + -
371A ILE* 3.7 27.3 - - + +
428A GLN* 4.3 12.8 - - - -
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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