Contacts of the strand formed by residues 196 - 199 (chain L) in PDB entry 6E07
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 ILE 196 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L ILE* 3.9 6.7 - - + -
169L VAL* 4.6 13.0 - - + -
187L ILE* 3.7 30.5 - - + +
188L SER* 4.6 4.3 - - - +
191L PHE* 3.9 24.7 - - + +
192L ARG 3.5 18.4 - - - +
193L GLU* 3.2 17.1 + - - +
194L ASP 3.6 0.4 - - - -
195L GLN* 1.3 78.4 - - - +
197L TYR* 1.3 66.5 + - - +
198L ARG* 3.6 50.4 + - + +
285L ARG* 5.3 1.4 + - - -
449L GLN* 2.8 21.1 + - - -
452L PHE* 5.3 1.4 - - - +
453L VAL 5.3 0.9 - - - +
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Residues in contact with TYR 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L ARG* 3.6 32.5 + - + -
167L ILE 2.9 15.8 + - - +
168L ILE* 3.3 13.4 - - + +
169L VAL 2.9 24.3 + - - -
194L ASP 4.0 8.0 + - - -
195L GLN 3.8 8.5 - - - -
196L ILE* 1.3 77.9 - - - +
198L ARG* 1.3 62.4 + - - +
199L ILE 3.6 1.4 + - - -
444L VAL* 3.6 35.2 - - + -
447L GLY* 3.4 30.1 + - - -
448L SER 3.7 14.6 - - - -
449L GLN* 3.4 33.3 - - + +
452L PHE* 3.7 28.4 - + + -
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Residues in contact with ARG 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L VAL* 3.6 9.6 - - + -
173L PHE* 3.9 24.5 - - + -
184L SER* 4.5 9.7 + - - +
187L ILE* 5.4 8.7 - - - +
188L SER* 4.7 4.6 + - - -
193L GLU* 2.9 28.5 + - - -
196L ILE* 3.6 36.1 + - + +
197L TYR* 1.3 70.5 - - - +
199L ILE* 1.3 63.2 - - - +
452L PHE* 3.4 12.3 - - - +
453L VAL* 2.9 62.1 + - + +
455L SER* 2.8 30.9 + - - +
458L LEU* 3.6 28.3 - - - +
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Residues in contact with ILE 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139L TYR* 4.3 13.5 - - + +
168L ILE* 3.6 27.6 - - + -
169L VAL 2.9 16.9 + - - +
170L GLU* 4.0 19.7 - - - +
171L LYS* 3.7 14.6 + - - +
173L PHE* 3.7 16.6 - - - -
198L ARG* 1.3 72.5 - - - +
200L ASP* 1.3 63.3 + - - +
201L HIS* 3.5 26.2 - - + +
437L TYR* 4.2 7.0 - - + +
440L LEU* 4.0 19.7 - - + -
441L ILE* 5.9 1.6 - - + +
444L VAL* 6.0 0.2 - - + -
452L PHE* 3.5 26.5 - - + -
453L VAL* 4.6 0.8 - - - +
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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