Contacts of the strand formed by residues 5118 - 5123 (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 TYR5118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4184D HIS* 4.9 8.9 + - - -
4278D THR* 4.7 0.5 - - - -
582E SIA 4.1 23.0 + - + +
5052E GLY* 3.4 29.4 - - - -
5053E ILE 3.2 6.7 - - - +
5054E PRO* 3.6 27.9 - - + +
5055E PHE* 3.4 6.3 - - - -
5058E PRO* 5.0 1.1 - - + +
5084E PRO* 3.7 35.2 - - + -
5085E PRO* 4.4 3.1 - - + -
5115E ASP* 2.8 54.6 + - - -
5116E CYS* 2.8 19.8 + - - +
5117E LEU* 1.3 74.6 - - - +
5119E LEU* 1.3 62.4 + - - +
5149E ALA* 5.3 0.2 - - - +
5168E ILE 3.9 0.2 - - - -
5169E GLN* 3.1 29.4 + - - +
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Residues in contact with LEU5119 (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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5052E GLY 3.6 0.3 + - - -
5053E ILE* 2.9 50.1 + - + +
5055E PHE* 3.9 23.1 - - + -
5118E TYR* 1.3 76.5 - - - +
5120E ASN* 1.3 64.2 + - - +
5121E ILE* 3.6 33.4 - - + -
5149E ALA* 5.7 0.7 - - - -
5166E VAL* 4.2 8.5 - - + -
5167E THR 3.2 12.6 - - - +
5168E ILE* 3.9 20.0 - - + -
5197E ALA* 4.5 8.3 - - + +
5200E TRP* 3.6 27.1 - - + -
5201E VAL* 4.8 0.2 - - + -
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Residues in contact with ASN5120 (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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5050E PHE 3.3 6.1 - - - +
5051E LEU* 3.4 16.7 - - + +
5052E GLY 2.8 30.0 + - - -
5083E TYR* 4.6 0.2 - - - -
5084E PRO* 3.6 10.7 - - - +
5119E LEU* 1.3 75.3 - - - +
5121E ILE* 1.3 63.3 + - - +
5122E TYR* 3.9 17.7 + - + -
5149E ALA* 4.2 4.2 - - - +
5150E SER* 3.4 35.8 + - - +
5165E VAL 3.8 0.9 - - - +
5166E VAL* 3.3 5.9 - - - +
5167E THR* 2.8 47.7 + - - +
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Residues in contact with ILE5121 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5048E ALA 3.5 1.6 - - - +
5049E ILE* 3.3 6.1 - - - +
5050E PHE* 2.8 47.6 + - + +
5053E ILE* 3.7 22.9 - - + -
5119E LEU* 3.6 11.4 - - + -
5120E ASN* 1.3 78.1 - - - +
5122E TYR* 1.3 71.1 + - - +
5123E THR* 4.3 2.9 - - - +
5164E VAL* 4.0 22.9 - - + -
5165E VAL 3.6 2.9 - - - +
5166E VAL* 4.2 8.3 - - + -
5200E TRP* 3.7 28.7 - - + -
5205E ILE* 4.3 6.1 - - + -
5208E PHE* 4.0 30.5 - - + -
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Residues in contact with TYR5122 (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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5047E VAL* 4.0 7.6 - - + -
5048E ALA 3.7 3.6 - - - -
5049E ILE* 3.7 37.9 - - + -
5051E LEU* 3.9 14.5 - - + +
5083E TYR* 4.5 2.4 + - - -
5104E ARG* 4.1 9.2 + - - -
5120E ASN* 3.9 25.3 + - + +
5121E ILE* 1.3 76.2 - - - +
5123E THR* 1.3 59.9 + - - +
5124E PRO* 4.3 0.4 - - - -
5150E SER* 5.4 0.3 + - - -
5152E TYR 3.7 13.0 + - - -
5153E ASP* 3.3 20.9 - - - -
5154E GLY* 3.5 33.7 - - - +
5155E LEU* 3.6 13.5 - - - -
5158E ALA* 3.7 8.2 - - + +
5164E VAL* 3.5 1.9 - - - -
5165E VAL* 2.8 46.2 + - + +
5167E THR* 4.2 9.9 - - + -
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Residues in contact with THR5123 (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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5047E VAL* 3.5 3.7 - - - +
5048E ALA* 2.9 53.8 + - + +
5050E PHE* 4.1 11.9 - - + -
5121E ILE* 4.5 3.4 - - + -
5122E TYR* 1.3 73.9 - - - +
5124E PRO* 1.3 64.2 - - - +
5125E ALA* 3.2 17.4 + - - +
5127E LEU* 4.4 10.5 - - + -
5164E VAL* 3.6 16.9 - - - +
5208E PHE* 2.7 32.8 + - + +
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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