Contacts of the helix formed by residues 5090 - 5102 (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 ASP5090 (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 2.5 79.5 + - - +
5089E GLN* 1.3 73.3 - - - +
5091E PRO* 1.3 65.6 - - - +
5092E LYS* 3.1 13.9 + - - +
5093E ALA* 3.3 3.6 + - + +
5094E GLY* 2.9 25.5 + - - -
5145E MET 5.1 0.2 + - - -
5146E VAL* 4.4 1.6 - - + +
5295E LEU* 4.0 8.4 - - - +
5298E THR* 5.1 7.4 - - + +
5299E LEU* 4.2 14.3 - - + +
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Residues in contact with PRO5091 (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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5086E MET* 4.7 6.3 - - + +
5089E GLN 2.8 10.2 - - - +
5090E ASP* 1.3 88.3 - - - +
5092E LYS* 1.3 65.0 + - + +
5094E GLY 3.9 0.2 - - - -
5095E GLN* 3.0 32.3 + - - +
5112E LEU* 3.8 29.6 - - + -
5295E LEU* 4.5 12.3 - - + -
5299E LEU* 5.2 4.7 - - + -
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Residues in contact with LYS5092 (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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3300C LYS 3.1 23.5 + - - +
3301C MET* 3.4 6.7 + - - +
3302C LYS* 2.9 63.6 - - + +
3309C GLN* 5.7 2.6 - - - +
5E COA 3.8 13.5 - - + +
5090E ASP* 3.1 6.7 + - - +
5091E PRO* 1.3 81.3 - - + +
5093E ALA* 1.3 61.7 + - - +
5095E GLN* 3.4 6.5 + - - +
5096E LEU* 3.0 30.9 + - - +
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Residues in contact with ALA5093 (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 2.8 78.8 + - + +
5090E ASP* 3.3 9.1 + - + +
5092E LYS* 1.3 80.6 - - - +
5094E GLY* 1.3 61.1 + - - +
5096E LEU* 3.4 4.9 + - - +
5097E LEU 3.1 18.9 + - - -
5146E VAL* 4.2 2.5 - - + -
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Residues in contact with GLY5094 (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 4.7 0.7 - - - -
5086E MET* 4.6 9.7 - - - +
5089E GLN* 3.2 26.7 - - - -
5090E ASP 2.9 13.3 + - - -
5091E PRO 4.1 0.9 - - - -
5093E ALA* 1.3 75.6 - - - +
5095E GLN* 1.3 63.5 + - - +
5097E LEU* 3.6 2.6 + - - +
5098E SER* 3.1 24.3 + - - -
5146E VAL* 4.2 7.8 - - - +
5147E GLY* 4.9 3.3 + - - -
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Residues in contact with GLN5095 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3309C GLN* 3.5 35.7 + - + +
5086E MET* 4.7 5.5 - - + +
5091E PRO 3.0 20.7 + - - +
5092E LYS* 3.8 6.7 - - - +
5094E GLY* 1.3 76.1 - - - +
5096E LEU* 1.3 62.5 + - - +
5098E SER* 3.4 6.8 + - - -
5099E GLU* 3.0 33.2 + - - +
5107E ASN* 4.5 8.2 + - - +
5109E PRO* 5.4 15.0 - - + +
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Residues in contact with LEU5096 (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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3308C LEU* 4.7 26.2 - - + +
3309C GLN* 5.1 10.2 - - + +
5E COA 3.8 38.4 - - + +
5092E LYS 3.0 18.2 + - - +
5093E ALA* 3.7 5.6 - - - +
5094E GLY 3.3 0.2 - - - -
5095E GLN* 1.3 77.6 - - - +
5097E LEU* 1.3 62.2 + - - +
5099E GLU* 3.2 15.6 + - + +
5100E LEU* 3.0 48.8 + - + +
5361E MET* 4.6 4.5 - - + -
5363E LEU* 3.9 14.4 - - + -
5459E MET* 5.7 3.1 - - + -
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Residues in contact with LEU5097 (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 3.1 53.8 + - - +
5093E ALA 3.1 8.8 + - - +
5094E GLY* 4.0 4.3 - - - +
5096E LEU* 1.3 77.2 - - - +
5098E SER* 1.3 65.4 + - - +
5100E LEU* 3.0 8.0 + - + +
5101E PHE* 2.9 64.4 + - + +
5141E GLY 4.1 7.6 - - - +
5142E GLY* 3.9 10.3 - - - +
5146E VAL* 3.8 12.3 - - + -
5147E GLY* 4.5 9.4 - - - -
5152E TYR* 5.5 2.0 - - - +
5358E LEU* 4.9 0.2 - - + -
5363E LEU* 4.5 6.1 - - + -
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Residues in contact with SER5098 (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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5086E MET* 6.2 2.2 - - - -
5094E GLY 3.1 17.9 + - - -
5095E GLN* 3.6 6.7 - - - -
5096E LEU 3.3 0.2 - - - -
5097E LEU* 1.3 77.5 - - - +
5099E GLU* 1.3 57.0 + - - +
5102E THR* 2.8 36.2 + - - -
5107E ASN* 2.7 27.6 + - - -
5108E ILE 4.8 3.3 + - - -
5110E LEU* 5.2 5.6 - - - +
5148E ALA* 6.1 0.7 - - - -
5151E THR* 2.7 32.8 + - - -
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Residues in contact with GLU5099 (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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3308C LEU 5.3 1.2 - - - +
3309C GLN* 2.8 48.7 + - - +
3310C GLY 5.1 0.7 + - - -
5095E GLN* 3.0 22.8 + - - +
5096E LEU* 3.5 13.8 - - + +
5098E SER* 1.3 78.5 - - - +
5100E LEU* 1.3 63.8 + - + +
5102E THR* 3.8 13.5 - - - +
5107E ASN* 3.4 30.5 - - + +
5482E LYS* 5.5 2.1 + - - -
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Residues in contact with LEU5100 (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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5096E LEU* 3.0 38.8 + - + +
5097E LEU* 3.0 9.2 + - - +
5099E GLU* 1.3 78.1 - - + +
5101E PHE* 1.3 72.5 + - + +
5357E TRP* 4.8 7.0 - - + -
5358E LEU* 3.5 26.0 - - + -
5361E MET* 3.7 20.4 - - + -
5363E LEU* 4.3 5.4 - - + -
5455E PHE 5.2 1.0 - - - +
5457E SER* 3.9 29.6 - - - +
5459E MET* 5.6 3.6 - - + -
5473E PHE* 3.4 21.6 - - - -
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Residues in contact with PHE5101 (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 4.9 6.1 - - - -
5097E LEU* 2.9 38.7 + - + +
5100E LEU* 1.3 89.5 - - + +
5102E THR* 1.3 68.1 + - - +
5103E ASN* 3.5 3.3 + - - +
5141E GLY 5.8 3.1 - - - -
5151E THR* 4.0 6.5 - - + -
5152E TYR* 3.5 37.1 - - - +
5220E GLU* 3.8 22.2 - - - -
5358E LEU* 3.4 41.3 - - + -
5468E HIS* 4.4 7.9 - + - -
5469E GLY* 4.3 17.3 - - - -
5472E LEU* 3.7 23.0 - - + +
5473E PHE* 4.4 10.2 - + - -
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Residues in contact with THR5102 (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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5098E SER 2.8 24.1 + - - +
5099E GLU* 3.8 14.7 - - - +
5100E LEU 3.8 0.2 - - - -
5101E PHE* 1.3 74.0 - - - +
5103E ASN* 1.3 58.1 + - - +
5104E ARG* 2.8 43.1 + - + +
5107E ASN* 3.9 25.4 + - + +
5151E THR* 2.9 23.8 + - - +
5473E PHE* 3.5 7.8 - - - -
5482E LYS* 3.1 18.5 - - - +
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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