Contacts of the strand formed by residues 5164 - 5168 (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 VAL5164 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5121E ILE* 4.0 15.9 - - + -
5122E TYR 3.5 10.8 - - - +
5123E THR* 3.6 23.6 - - - +
5124E PRO* 4.3 0.2 - - - -
5133E LEU* 4.2 9.6 - - + -
5134E PRO 2.9 11.1 + - - +
5135E VAL* 3.4 8.8 - - + +
5136E MET* 2.8 28.2 + - - +
5163E VAL* 1.3 72.3 - - - +
5165E VAL* 1.3 60.7 + - - +
5166E VAL* 4.2 4.7 - - + -
5205E ILE* 4.0 26.0 - - + -
5208E PHE 4.0 4.0 - - - +
5209E GLY 4.0 5.8 - - - +
5210E GLY* 3.9 23.6 - - - -
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Residues in contact with VAL5165 (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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5121E ILE* 3.6 2.4 - - - +
5122E TYR* 2.8 46.0 + - + +
5136E MET* 3.4 9.9 - - + +
5154E GLY* 4.0 24.0 - - - +
5157E LEU* 3.8 32.8 - - + -
5158E ALA* 3.9 12.6 - - + +
5163E VAL* 3.9 12.6 - - + -
5164E VAL* 1.3 74.0 - - - +
5166E VAL* 1.3 70.2 + - - +
5167E THR* 4.5 10.3 - - + -
5218E PHE* 4.9 4.3 - - + -
5476E PHE* 4.6 12.1 - - + -
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Residues in contact with VAL5166 (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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5119E LEU* 4.2 21.5 - - + -
5120E ASN 3.3 9.0 - - - +
5121E ILE* 4.2 7.6 - - + -
5135E VAL* 4.0 15.0 - - + -
5136E MET 2.9 6.9 + - - +
5137E VAL* 3.3 13.2 - - + +
5138E TRP* 2.7 32.9 + - - +
5164E VAL* 4.2 4.0 - - + -
5165E VAL* 1.3 78.3 - - - +
5167E THR* 1.3 59.8 + - - +
5168E ILE* 3.9 20.4 - - + -
5200E TRP* 5.8 0.2 - - + -
5201E VAL* 4.4 10.3 - - + -
5205E ILE* 4.0 27.4 - - + -
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Residues in contact with THR5167 (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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5119E LEU* 3.2 3.5 - - - +
5120E ASN* 2.8 53.6 + - - +
5122E TYR* 4.2 6.3 - - + -
5138E TRP* 3.8 26.9 - - + -
5149E ALA* 3.7 19.8 + - - +
5152E TYR* 3.8 23.1 + - + +
5154E GLY 5.3 0.2 - - - +
5165E VAL* 4.5 13.0 - - + -
5166E VAL* 1.3 74.7 - - - +
5168E ILE* 1.3 62.0 + - - +
5476E PHE* 5.0 2.2 - - + -
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Residues in contact with ILE5168 (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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5055E PHE* 4.8 0.2 - - + -
5118E TYR 4.0 4.5 - - - +
5119E LEU* 3.9 15.0 - - + -
5137E VAL* 3.9 21.8 - - + -
5138E TRP* 3.3 17.6 + - - +
5139E ILE* 4.0 24.5 - - + -
5140E HIS* 3.7 14.2 + - - -
5149E ALA* 3.5 9.8 - - - +
5166E VAL* 3.9 7.6 - - + -
5167E THR* 1.3 78.1 - - - +
5169E GLN* 1.3 69.0 + - - +
5170E TYR* 4.5 1.9 - - + -
5194E GLN* 4.1 26.9 - - + +
5197E ALA* 3.8 35.0 - - + -
5198E LEU* 5.8 1.8 - - + -
5201E VAL* 5.7 0.4 - - + -
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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