Contacts of the helix formed by residues 5221 - 5233 (chain E) in PDB entry 2H7C
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 SER5221 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E COA 3.3 27.2 + - - +
5101E PHE* 5.9 0.2 - - - -
5141E GLY* 4.4 3.8 - - - -
5220E GLU* 1.3 80.6 - - - +
5222E ALA* 1.3 64.1 + - - -
5223E GLY 2.9 0.7 - - - -
5224E GLY* 2.7 21.5 + - - -
5225E GLU* 2.8 10.7 + - - +
5246E GLU 2.8 13.3 + - - -
5247E SER 3.1 15.4 + - - -
5248E GLY* 3.7 6.5 - - - -
5255E LEU* 4.7 4.3 - - - +
5426E PHE* 4.7 2.6 - - - -
5468E HIS* 2.8 30.4 + - - -
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Residues in contact with ALA5222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E COA 5.6 0.2 - - - -
5140E HIS 4.3 0.7 - - - -
5141E GLY* 4.0 1.7 - - - -
5142E GLY 3.9 4.9 - - - +
5143E GLY* 3.5 30.7 - - - +
5144E LEU* 3.6 27.4 - - + +
5170E TYR* 4.7 1.3 - - - +
5220E GLU 3.2 0.4 + - - -
5221E SER* 1.3 81.8 + - - +
5223E GLY* 1.3 58.4 + - - +
5225E GLU* 3.4 3.5 + - - +
5226E SER* 2.9 31.6 + - - -
5255E LEU* 3.8 17.5 - - + +
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Residues in contact with GLY5223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5139E ILE* 3.2 31.7 - - - +
5140E HIS 3.4 11.0 + - - -
5219E GLY* 3.7 7.8 - - - -
5220E GLU 2.9 8.4 + - - -
5222E ALA* 1.3 78.7 - - - +
5224E GLY* 1.3 58.7 + - - +
5226E SER* 3.4 3.0 + - - -
5227E VAL* 3.0 31.4 + - - +
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Residues in contact with GLY5224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5219E GLY 3.4 17.2 - - - -
5220E GLU 3.5 6.3 - - - -
5221E SER 2.7 17.2 + - - -
5223E GLY* 1.3 71.1 - - - +
5225E GLU* 1.3 57.6 + - - -
5227E VAL* 3.3 2.0 + - - -
5228E SER* 3.0 15.2 + - - -
5245E SER* 2.8 26.9 + - - -
5246E GLU 4.3 0.9 - - - -
5248E GLY 2.9 17.0 - - - +
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Residues in contact with GLU5225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5144E LEU* 4.2 4.8 - - - +
5191E HIS* 3.7 6.8 - - - -
5221E SER 2.8 5.9 + - - +
5222E ALA 3.6 7.1 - - - +
5224E GLY* 1.3 77.9 - - - +
5226E SER* 1.3 62.9 + - - +
5228E SER* 3.2 2.6 + - - -
5229E VAL* 2.8 39.3 + - - +
5248E GLY 3.3 1.2 + - - -
5249E VAL 3.4 32.8 - - - +
5250E ALA* 4.1 5.2 - - - -
5255E LEU* 3.5 46.8 - - + +
5256E VAL* 3.6 8.8 - - + +
5321E THR* 2.7 32.1 + - - -
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Residues in contact with SER5226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5139E ILE* 4.0 7.6 - - - +
5144E LEU* 4.0 5.4 - - - +
5170E TYR* 4.8 0.2 + - - -
5191E HIS* 3.3 18.2 - - - -
5194E GLN* 3.1 37.7 + - - +
5222E ALA 2.9 24.1 + - - -
5223E GLY* 3.5 6.8 - - - -
5225E GLU* 1.3 78.4 + - - +
5227E VAL* 1.3 64.5 + - - +
5229E VAL* 3.2 3.2 + - - +
5230E LEU* 2.9 30.1 + - - +
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Residues in contact with VAL5227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5139E ILE* 4.3 9.0 - - + -
5217E ILE* 4.0 19.5 - - + +
5218E PHE* 3.8 9.6 - - - +
5219E GLY 3.8 11.4 - - - +
5223E GLY 3.0 19.3 + - - +
5224E GLY 3.3 8.0 + - - +
5226E SER* 1.3 75.4 - - - +
5228E SER* 1.3 63.7 + - - +
5230E LEU* 3.1 6.0 + - - +
5231E VAL* 3.0 23.0 + - - +
5243E ALA* 3.8 29.2 - - + -
5244E ILE 3.7 21.5 - - - +
5245E SER* 3.4 12.6 - - - +
5346E TYR* 4.1 3.1 - - + -
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Residues in contact with SER5228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5224E GLY 3.0 11.9 + - - -
5225E GLU 3.4 4.3 - - - -
5227E VAL* 1.3 79.0 - - - +
5229E VAL* 1.3 60.5 + - - +
5231E VAL* 3.4 5.6 + - - +
5232E LEU* 3.4 25.6 + - - +
5249E VAL* 3.6 8.2 - - - +
5250E ALA* 2.8 38.8 + - - +
5346E TYR* 3.4 24.0 + - - -
5433E VAL* 4.6 8.3 - - - +
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Residues in contact with VAL5229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5191E HIS* 4.5 8.7 - - + +
5225E GLU* 2.8 41.2 + - - +
5226E SER* 3.2 7.2 + - - +
5228E SER* 1.3 75.3 - - - +
5230E LEU* 1.3 66.2 + - + +
5232E LEU* 3.1 9.4 + - - +
5233E SER* 3.0 19.9 + - - -
5250E ALA* 4.2 14.6 - - + -
5256E VAL* 5.5 1.3 - - + -
5321E THR* 4.3 11.0 - - + +
5327E LEU* 3.6 34.3 - - + -
5328E LEU* 4.0 18.1 - - + +
5332E PRO* 5.7 0.9 - - + -
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Residues in contact with LEU5230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5139E ILE* 3.8 27.4 - - + -
5191E HIS* 4.6 6.5 - - + +
5194E GLN* 4.3 13.5 - - + +
5195E VAL* 3.7 31.6 - - + +
5198E LEU* 4.2 17.9 - - + -
5217E ILE* 4.2 16.2 - - + -
5226E SER 2.9 21.3 + - - +
5227E VAL 3.5 4.5 - - - +
5229E VAL* 1.3 74.6 - - + +
5231E VAL* 1.3 65.4 + - - +
5233E SER* 3.2 13.3 + - - +
5236E ALA* 3.6 29.8 - - + +
5240E PHE* 3.7 5.8 - - + -
5327E LEU* 4.7 10.3 - - + -
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Residues in contact with VAL5231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5227E VAL 3.0 18.6 + - - +
5228E SER* 3.6 11.0 - - - +
5229E VAL 3.2 0.2 - - - -
5230E LEU* 1.3 77.6 - - - +
5232E LEU* 1.3 61.1 + - + +
5233E SER 3.7 1.2 + - - +
5240E PHE* 3.8 17.8 - - + -
5243E ALA* 3.9 27.1 - - + -
5341E PHE* 3.2 36.2 - - + +
5342E HIS 4.5 7.3 - - - +
5344E VAL* 4.7 7.4 - - + -
5346E TYR* 4.4 21.1 - - + -
5437E HIS* 4.6 10.8 - - + +
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Residues in contact with LEU5232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5228E SER* 3.4 17.0 - - - +
5229E VAL* 3.1 9.4 + - - +
5231E VAL* 1.3 80.7 - - + +
5233E SER* 1.3 57.4 + - - +
5234E PRO* 3.7 6.9 - - - +
5250E ALA* 4.0 11.2 - - + -
5328E LEU* 4.3 5.7 - - + +
5332E PRO* 3.8 36.6 - - + +
5335E LEU* 3.9 38.0 - - + +
5336E GLN* 4.7 9.2 - - + -
5340E ASN* 4.3 9.4 + - - -
5341E PHE* 3.7 41.3 - - + +
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Residues in contact with SER5233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5229E VAL 3.0 14.1 + - - -
5230E LEU* 3.2 15.0 + - - +
5231E VAL 3.4 1.2 - - - +
5232E LEU* 1.3 78.3 - - - +
5234E PRO* 1.3 67.3 - - - +
5235E LEU* 3.2 14.4 + - - +
5236E ALA* 3.2 12.5 + - - -
5237E LYS* 3.7 7.4 + - - +
5327E LEU* 2.7 47.5 + - - +
5328E LEU* 4.8 0.7 - - - -
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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