Contacts of the helix formed by residues 194 - 200 (chain L) in PDB entry 3Q3G
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 ASN 194 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192L ASN* 2.8 33.0 + - - +
193L PRO* 1.3 78.9 - - - +
195L PRO* 1.4 67.8 - - - +
196L ARG 3.4 2.0 - - - -
197L SER* 3.2 27.3 + - - +
198L LEU* 3.3 18.0 + - - +
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Residues in contact with PRO 195 (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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158L SER* 3.8 13.5 - - - +
161L MET* 3.6 53.5 - - + +
162L GLU* 3.9 21.5 - - + +
165L LYS* 4.6 9.2 - - - +
189L PHE* 4.5 8.3 - - + -
193L PRO 3.4 11.9 - - - +
194L ASN* 1.4 80.9 - - - +
196L ARG* 1.3 58.0 + - - +
198L LEU* 3.3 7.2 + - + +
199L VAL* 3.0 29.8 + - - +
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Residues in contact with ARG 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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155L GLU* 2.6 32.9 + - - -
158L SER* 3.4 33.1 + - - +
159L THR* 3.2 20.6 + - - +
162L GLU* 2.8 39.6 + - - +
194L ASN 3.4 0.8 - - - -
195L PRO* 1.3 73.2 - - - +
197L SER* 1.3 63.1 + - - +
199L VAL 4.0 0.2 - - - -
200L LYS* 3.2 28.8 + - - +
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Residues in contact with SER 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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192L ASN* 3.3 17.1 + - - -
194L ASN* 3.2 30.2 + - - +
196L ARG* 1.3 77.7 - - - +
198L LEU* 1.4 57.2 + - - +
200L LYS* 4.7 3.9 - - - +
201L PRO* 3.3 19.9 - - - +
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Residues in contact with LEU 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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183L HIS* 5.2 2.5 - - - +
184L PHE* 3.7 43.2 - - + -
188L GLU* 4.5 12.8 - - + +
189L PHE* 3.5 27.1 - - + -
192L ASN* 3.4 41.3 - - + +
194L ASN 3.5 12.8 - - - +
195L PRO* 3.3 7.0 + - + +
197L SER* 1.4 75.1 - - - +
199L VAL* 1.3 61.5 + - - +
201L PRO* 3.6 11.9 - - - +
202L ILE* 3.7 14.0 - - - +
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Residues in contact with VAL 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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154L LYS* 3.4 37.8 - - + +
157L VAL* 4.1 14.6 - - + -
158L SER* 3.3 24.7 - - - +
161L MET* 3.5 28.5 - - + -
173L LEU* 4.6 0.7 - - + -
184L PHE* 4.1 7.0 - - + -
195L PRO 3.0 6.6 + - - +
196L ARG 4.7 0.2 - - - +
198L LEU* 1.3 75.5 - - - +
200L LYS* 1.3 68.3 + - - +
202L ILE* 3.0 39.2 + - + +
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Residues in contact with LYS 200 (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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154L LYS* 2.8 25.0 + - - +
196L ARG 3.2 21.3 + - - +
197L SER* 5.1 3.4 - - - +
199L VAL* 1.3 76.6 - - - +
201L PRO* 1.4 68.3 - - + +
202L ILE 4.0 0.2 - - - +
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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