Contacts of the strand formed by residues 198 - 202 (chain F) in PDB entry 3J8B
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 198 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124F VAL* 6.3 2.5 - - + -
170F LEU* 3.4 23.4 + - + +
171F GLY* 3.1 2.3 - - - -
172F TRP* 2.9 27.5 + - - +
196F ASN 4.7 1.8 - - - +
197F PRO* 1.3 75.8 - - - +
199F HIS* 1.3 61.1 + - - +
200F LEU 4.1 0.2 - - - -
216F TYR 3.6 6.7 - - - +
217F VAL* 4.9 3.1 - - + +
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Residues in contact with HIS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F TRP* 3.4 6.7 - - + +
183F SER* 6.4 2.0 - - - -
187F HIS* 5.9 7.6 - - + -
197F PRO 4.4 0.2 + - - -
198F ILE* 1.3 73.6 - - - +
200F LEU* 1.3 61.1 + - - +
201F THR 4.0 0.6 + - - -
214F LYS 3.6 1.7 - - - +
215F ALA* 3.4 5.2 - - - +
216F TYR* 2.8 48.1 + - + +
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F LEU* 5.5 7.9 - - + -
172F TRP 2.9 13.9 + - - +
173F TYR* 2.9 36.3 - - + +
174F ALA 3.1 3.4 + - - -
198F ILE 4.1 0.6 + - - -
199F HIS* 1.3 72.6 - - - +
201F THR* 1.3 63.1 + - - +
202F VAL* 6.1 1.1 - - + -
213F ILE* 5.9 4.7 - - + -
214F LYS 3.5 5.2 - - - -
215F ALA* 4.7 4.0 - - + +
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Residues in contact with THR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F ALA* 3.4 10.3 - - - +
176F GLY* 5.1 8.1 - - - -
177F HIS 4.8 13.7 - - - -
178F ASP* 5.5 6.1 - - - -
179F ILE 5.7 0.9 - - - -
199F HIS* 4.0 1.2 - - - +
200F LEU* 1.3 73.6 - - - +
202F VAL* 1.3 60.6 + - - +
203F ASP 3.9 1.4 + - - -
213F ILE* 3.1 7.3 - - - +
214F LYS* 2.8 52.7 + - - +
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Residues in contact with VAL 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F LEU* 5.5 8.1 - - + +
102F ILE* 3.9 28.2 - - + +
173F TYR* 5.6 3.8 - - + -
174F ALA 2.9 12.0 + - - +
175F THR* 3.2 23.5 - - - -
200F LEU* 3.6 3.8 + - + +
201F THR* 1.3 72.1 - - - +
203F ASP* 1.3 61.5 + - - +
204F THR* 2.9 10.7 + - - +
212F SER* 3.0 10.3 - - - +
213F ILE* 4.5 2.2 - - + +
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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