Contacts of the strand formed by residues 298 - 302 (chain P) in PDB entry 3K9Q
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 ARG 298 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O LEU* 4.6 12.1 - - + +
209O ASN 5.5 2.4 + - - -
210O SER* 4.9 18.2 - - - +
229O ASP* 4.4 19.3 + - - +
230O GLY* 4.7 17.2 + - - +
231O GLY* 5.6 3.6 - - - -
256P VAL* 4.2 3.8 - - - -
295P THR 3.6 22.8 + - - -
296P GLN* 3.6 9.8 + - - +
297P THR* 1.3 87.4 + - - +
299P VAL* 1.3 70.0 + - - +
300P MET 4.1 0.2 - - - -
307P LEU 3.8 0.9 - - - +
308P VAL* 3.6 1.4 - - - +
309P LYS* 2.9 44.8 + - + +
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Residues in contact with VAL 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173O LEU* 5.6 0.4 - - - -
229O ASP* 5.7 0.9 - - - +
254P VAL* 3.4 20.9 - - + +
255P THR* 3.9 6.7 - - - +
256P VAL* 3.7 36.1 - - + +
259P VAL* 5.1 0.2 - - + -
297P THR* 5.1 1.3 - - + -
298P ARG* 1.3 83.3 - - - +
300P MET* 1.3 60.4 + - - +
301P SER* 3.8 9.1 + - - +
306P GLN* 3.6 20.0 - - - +
307P LEU 3.5 6.7 - - - +
308P VAL* 4.1 21.1 - - + -
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Residues in contact with MET 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O GLU* 3.5 23.1 - - + +
172O GLY 4.0 8.1 - - - +
173O LEU* 3.8 20.1 - - + +
226O GLY 3.8 15.0 - - - +
227O LYS 3.8 10.3 - - - +
228O LEU* 3.3 22.4 - - - +
229O ASP* 3.2 36.3 - - + +
298P ARG 4.1 0.4 - - - -
299P VAL* 1.3 74.1 - - - +
301P SER* 1.3 64.7 + - - +
302P VAL* 3.9 9.4 - - - -
306P GLN* 3.0 8.1 - - - +
307P LEU* 2.9 39.7 + - + +
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Residues in contact with SER 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226O GLY 5.1 1.2 - - - +
299P VAL* 3.8 8.8 + - - +
300P MET* 1.3 78.6 - - - +
302P VAL* 1.3 66.0 + - - +
303P GLY 4.1 8.9 + - - -
305P ARG 3.5 3.6 - - - -
306P GLN* 2.9 32.3 + - - +
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Residues in contact with VAL 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O VAL* 3.9 21.1 - - + +
171O GLU* 3.3 27.1 + - + +
226O GLY 4.1 12.6 - - - +
227O LYS* 4.2 17.0 - - + -
300P MET* 3.9 12.6 - - - -
301P SER* 1.3 77.4 - - - +
303P GLY* 1.3 67.4 + - - +
304P ASP 3.1 0.5 + - - -
305P ARG* 2.8 31.9 + - - +
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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