Contacts of the strand formed by residues 189 - 193 (chain o) in PDB entry 6FF7
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 PHE 189 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188o SER* 1.3 71.5 - - - +
190o HIS* 1.3 61.6 + - - +
191o ARG 3.4 3.3 + - - +
192o ILE* 5.3 6.0 + - + +
198o CYS* 5.1 10.1 - - + -
199o GLN 3.2 22.0 - - - +
200o GLY* 4.1 2.7 - - - -
278o ILE* 5.8 4.0 - - + -
288o PRO* 4.3 15.2 - - - +
292o VAL* 2.9 32.9 + - + +
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Residues in contact with HIS 190 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188o SER* 3.5 12.0 + - - +
189o PHE* 1.3 74.0 - - - +
191o ARG* 1.3 60.4 + - + +
192o ILE 4.3 0.4 - - - -
199o GLN 3.0 5.6 + - - +
200o GLY* 4.6 1.3 - - - -
202o ASP* 5.9 3.1 - - + -
206o HIS* 3.5 30.7 - - - +
207o ASN* 4.4 10.1 - - - -
208o GLY 5.2 0.7 - - - +
286o GLY 3.8 7.8 - - - +
287o LYS* 5.0 1.6 - - - -
288o PRO* 4.7 8.4 - - - +
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Residues in contact with ARG 191 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189o PHE 3.4 1.0 - - - -
190o HIS* 1.3 81.4 - - + +
192o ILE* 1.3 58.5 + - - +
193o ILE* 4.2 0.7 - - - -
197o MET 4.1 0.9 - - - +
198o CYS* 3.7 0.7 - - - -
199o GLN* 2.8 48.4 + - + +
286o GLY* 3.3 11.7 - - - +
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Residues in contact with ILE 192 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189o PHE* 5.3 6.5 - - + +
190o HIS 4.3 0.2 - - - -
191o ARG* 1.3 74.8 - - - +
193o ILE* 1.3 60.2 + - - +
197o MET 3.7 5.6 - - - +
198o CYS* 4.4 9.9 - - + +
278o ILE 4.6 10.8 - - - +
279o GLU* 5.3 2.9 - - - +
281o GLN* 4.6 2.9 - - + +
282o GLY* 3.7 19.5 - - - +
283o SER 3.1 25.1 + - - +
286o GLY* 2.8 17.2 + - - +
288o PRO* 5.1 9.2 - - + -
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Residues in contact with ILE 193 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191o ARG 4.2 0.8 - - - -
192o ILE* 1.3 73.4 - - - +
194o PRO* 1.3 66.3 - - - +
195o GLN 3.5 0.2 + - - -
196o PHE* 3.1 28.7 + - + -
197o MET 2.9 19.1 + - - +
252o CYS* 5.0 1.0 - - - +
279o GLU* 5.4 2.5 - - - +
282o GLY* 5.1 0.2 - - - -
283o SER 3.6 11.4 - - - +
284o LYS* 4.7 9.2 - - - +
286o GLY* 4.8 3.8 - - - -
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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