Contacts of the strand formed by residues 184 - 188 (chain E) in PDB entry 6UWZ
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 TRP 184 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E LEU* 4.5 9.2 - - + +
43E LEU* 3.7 34.4 + - + +
45E GLU* 3.5 9.3 + - + -
138E ASP* 3.7 4.9 - - - -
140E GLN* 3.4 30.3 - - + -
180E GLU* 3.3 13.7 - - - +
181E ASN* 3.7 32.2 - - - +
182E GLY 3.8 0.2 - - - -
183E GLU* 1.3 99.8 + - + +
185E THR* 1.3 61.7 + - - +
186E ILE* 5.1 0.9 - - - +
215E ILE* 3.5 43.3 - - + -
216E GLN 3.6 1.6 - - - -
217E ARG* 3.3 70.2 - - + -
218E LYS* 3.6 7.4 + - - -
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Residues in contact with THR 185 (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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180E GLU* 3.8 12.7 - - + +
184E TRP* 1.3 71.8 - - - +
186E ILE* 1.3 71.2 + - - +
187E ARG* 3.6 33.9 + - - +
215E ILE* 3.1 4.7 - - - -
216E GLN 2.7 44.0 + - - -
218E LYS* 3.1 32.4 + - - +
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Residues in contact with ILE 186 (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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37E LEU* 3.6 31.6 - - + -
40E LEU* 4.1 13.5 - - + -
173E ILE* 4.3 14.4 - - + -
178E PHE* 3.7 22.2 - - + -
180E GLU* 3.6 16.0 + - - +
184E TRP 5.1 0.7 - - - +
185E THR* 1.3 81.3 - - - +
187E ARG* 1.3 63.6 + - - +
188E HIS 3.6 20.6 - - - +
189E ARG* 4.6 3.8 - - + -
213E LEU* 3.9 14.1 - - + -
214E ILE 3.9 4.7 - - - +
215E ILE* 4.0 13.2 - - + -
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Residues in contact with ARG 187 (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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185E THR* 3.8 30.1 + - - +
186E ILE* 1.3 79.6 - - - +
188E HIS* 1.3 76.0 + - + +
189E ARG* 5.5 3.9 + - - +
214E ILE 3.0 10.0 + - - +
216E GLN* 3.4 32.2 - - + +
217E ARG 5.7 0.2 + - - -
475E VAL* 4.0 33.6 - - + +
488E VAL* 5.8 2.4 - - - +
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Residues in contact with HIS 188 (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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186E ILE* 3.6 8.1 - - - +
187E ARG* 1.3 86.0 - - + +
189E ARG* 1.3 66.3 + - - +
190E PRO* 3.6 7.0 - - + -
213E LEU* 3.9 1.0 - - - -
214E ILE* 3.3 44.0 + - + +
475E VAL* 3.9 19.9 - - + +
476E PRO* 3.1 26.4 + - + -
477E GLU 3.3 20.6 + - - -
478E PHE 3.9 11.7 - - - -
479E PRO* 3.8 26.3 - - + +
486E LYS 5.0 3.8 - - - -
488E VAL* 5.6 6.7 - - + -
1L NAG 5.2 1.0 + - - -
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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