Contacts of the strand formed by residues 195 - 198 (chain L) in PDB entry 5GJQ
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 195 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L MET 4.5 4.5 - - - +
123L SER* 4.6 6.8 - - - +
149L ILE* 5.5 0.2 - - + -
184L ALA 5.7 0.4 - - - -
187L VAL* 3.7 20.6 - - + -
188L ALA* 3.5 33.4 - - + -
191L LEU* 3.2 28.3 - - + -
192L ASP* 3.3 30.5 - - - -
193L CYS* 4.1 11.0 - - + -
194L ASN* 1.3 73.8 - - - +
196L LEU* 1.3 63.4 + - - +
197L LYS* 3.8 17.2 - - - +
229L ILE* 2.4 65.1 - - + +
231L PHE* 5.7 0.7 - - + -
276L ILE* 5.3 1.6 - - + -
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Residues in contact with LEU 196 (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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119L VAL* 5.9 2.2 - - + -
122L MET* 4.2 10.8 - - + +
123L SER* 3.1 28.9 - - - +
194L ASN* 3.0 35.2 - - - +
195L PHE* 1.3 75.5 - - - +
197L LYS* 1.3 64.0 + - - +
198L VAL* 3.7 10.1 + - + +
218L MET* 4.0 14.4 - - + +
221L TYR* 3.2 24.0 - - + -
222L ALA* 3.9 7.6 - - + -
228L CYS* 4.5 1.3 - - + -
229L ILE 2.5 9.3 + - - -
230L ILE* 3.0 32.3 - - + +
231L PHE 3.1 19.0 + - - +
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Residues in contact with LYS 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L MET* 4.0 28.5 + - - +
126L ASP* 4.0 15.6 + - - +
127L PRO 5.3 0.8 + - - -
184L ALA 3.9 5.3 + - - -
188L ALA* 3.5 31.1 - - - +
195L PHE* 3.8 22.2 - - - +
196L LEU* 1.3 72.0 - - - +
198L VAL* 1.3 63.6 + - - +
199L VAL* 4.0 3.8 + - + +
231L PHE* 2.8 36.1 - - + +
233L ASP* 6.3 0.4 - - + -
320M PHE* 2.7 51.9 - - + -
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Residues in contact with VAL 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L MET* 5.5 4.5 - - + -
196L LEU* 3.8 11.9 - - + +
197L LYS* 1.3 79.6 - - - +
199L VAL* 1.3 50.5 + - + +
200L SER* 2.7 15.7 + - - +
203L ILE* 2.6 48.2 - - + -
218L MET* 2.9 33.0 - - + -
230L ILE* 4.5 3.4 - - + -
231L PHE 2.5 10.0 + - - +
232L MET* 2.7 27.4 - - + +
233L ASP 2.6 26.3 + - - -
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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