Contacts of the strand formed by residues 5210 - 5220 (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 GLY5210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5132E ARG* 3.7 8.2 - - - -
5133E LEU 3.4 7.0 - - - -
5135E VAL* 3.8 13.5 - - - -
5164E VAL* 3.9 7.6 - - - -
5205E ILE* 3.1 15.1 + - - -
5206E ALA* 3.1 22.5 - - - -
5208E PHE 3.3 1.4 - - - -
5209E GLY* 1.3 82.5 - - - +
5211E ASN* 1.3 59.6 + - - -
5212E PRO* 3.2 4.3 - - - +
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Residues in contact with ASN5211 (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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5132E ARG* 3.3 36.5 + - + +
5133E LEU 2.7 14.5 + - - +
5135E VAL* 3.7 5.3 - - - +
5205E ILE* 4.1 1.8 - - - -
5210E GLY* 1.3 70.5 - - - -
5212E PRO* 1.3 63.6 - - - +
5213E GLY* 2.9 26.2 + - - -
5214E SER* 2.9 48.1 + - - +
5215E VAL* 4.0 0.3 - - - +
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Residues in contact with PRO5212 (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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5132E ARG* 4.4 7.2 - - - +
5202E GLN* 3.6 42.6 + - + +
5205E ILE* 3.6 17.4 - - + -
5206E ALA* 4.2 15.3 - - + -
5210E GLY 3.2 11.2 - - - +
5211E ASN* 1.3 86.9 - - - +
5213E GLY* 1.3 55.4 + - - +
5214E SER 3.2 1.1 - - - -
5215E VAL* 3.8 11.5 - - + +
5241E HIS* 3.3 17.0 - - - -
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Residues in contact with GLY5213 (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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5211E ASN* 2.9 16.9 + - - -
5212E PRO* 1.3 82.1 - - - +
5214E SER* 1.3 59.1 + - - +
5241E HIS* 3.3 28.1 + - - +
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Residues in contact with SER5214 (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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5134E PRO* 3.8 9.8 - - - +
5135E VAL 3.0 23.6 + - - +
5211E ASN* 2.9 31.5 + - - +
5212E PRO 3.2 0.2 - - - -
5213E GLY* 1.3 83.5 - - - +
5215E VAL* 1.3 58.2 + - - +
5216E THR* 5.2 1.2 + - - -
5241E HIS* 3.7 4.7 - - - -
5242E ARG* 4.2 13.2 + - - +
5504E ALA 3.5 19.9 + - - -
5505E ARG* 4.8 2.4 + - - -
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Residues in contact with VAL5215 (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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5135E VAL* 3.4 9.0 - - + +
5137E VAL* 3.8 27.6 - - + -
5198E LEU* 4.5 6.7 - - + -
5201E VAL* 4.1 22.0 - - + -
5202E GLN* 5.8 1.8 - - + +
5211E ASN 4.0 6.1 - - - +
5212E PRO* 3.8 20.9 - - + +
5214E SER* 1.3 76.2 - - - +
5216E THR* 1.3 65.5 + - - +
5239E LEU 4.0 23.1 - - - +
5240E PHE* 3.5 6.5 - - + +
5241E HIS* 2.7 40.7 + - - +
5242E ARG* 3.4 4.0 + - - -
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Residues in contact with THR5216 (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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5135E VAL 2.7 14.8 + - - -
5136E MET* 3.3 9.4 - - + -
5137E VAL* 2.7 33.6 + - - +
5214E SER 5.2 0.7 + - - -
5215E VAL* 1.3 75.1 - - - +
5217E ILE* 1.3 68.2 + - - +
5218E PHE* 3.9 1.1 + - + -
5242E ARG* 3.4 28.5 - - + +
5244E ILE* 4.2 22.7 - - + -
5503E PHE* 4.7 0.9 - - + -
5504E ALA* 3.2 38.4 + - + +
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Residues in contact with ILE5217 (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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5137E VAL* 3.4 12.3 - - + +
5139E ILE* 4.8 7.2 - - + -
5198E LEU* 3.6 34.3 - - + -
5215E VAL* 4.2 0.9 - - + -
5216E THR* 1.3 77.3 - - - +
5218E PHE* 1.3 59.6 + - - +
5227E VAL* 4.0 24.4 - - + +
5230E LEU* 4.2 20.6 - - + -
5240E PHE* 3.6 44.4 - - + -
5242E ARG 3.1 13.3 + - - +
5243E ALA* 3.3 5.2 - - + -
5244E ILE 2.9 24.6 + - - +
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Residues in contact with PHE5218 (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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5136E MET* 3.7 36.8 - - + -
5137E VAL 3.0 19.7 + - - +
5138E TRP* 3.2 62.3 - + + -
5139E ILE* 2.9 23.9 + - - +
5157E LEU* 4.2 12.8 - - + -
5165E VAL* 4.9 2.5 - - + -
5216E THR* 4.2 2.5 - - + -
5217E ILE* 1.3 77.4 - - - +
5219E GLY* 1.3 58.3 + - - +
5227E VAL* 3.8 5.2 - - - -
5244E ILE* 3.3 30.5 - - + -
5246E GLU* 3.9 9.4 - - - +
5475E VAL* 4.0 13.2 - - + -
5476E PHE* 4.0 14.4 - + - -
5500E TRP* 4.1 10.1 - + - -
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Residues in contact with GLY5219 (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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5138E TRP* 3.6 11.6 - - - -
5139E ILE 3.2 16.2 - - - -
5218E PHE* 1.3 77.7 - - - +
5220E GLU* 1.3 60.7 + - - -
5223E GLY 3.8 8.7 - - - -
5224E GLY* 3.4 9.4 - - - -
5227E VAL* 3.8 2.0 - - - +
5244E ILE 3.2 5.1 + - - -
5246E GLU* 2.9 28.0 + - - +
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Residues in contact with GLU5220 (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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5101E PHE* 3.8 16.1 - - - -
5138E TRP* 3.5 24.0 - - + -
5139E ILE 3.7 3.0 + - - -
5141E GLY* 3.2 14.4 + - - -
5152E TYR* 5.4 0.7 + - - -
5219E GLY* 1.3 73.0 - - - -
5221E SER* 1.3 76.4 + - - +
5223E GLY 2.9 15.4 + - - -
5224E GLY 3.5 2.2 - - - +
5246E GLU* 3.1 11.0 - - + +
5247E SER* 4.3 1.8 - - - -
5468E HIS* 3.2 28.3 + - - -
5469E GLY* 3.6 15.3 + - - -
5471E GLU* 3.1 25.1 - - - +
5472E LEU* 3.7 17.1 - - + +
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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