Contacts of the strand formed by residues 215 - 220 (chain D) 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 THR 215 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D PRO* 3.6 10.6 - - + +
130D PRO* 4.7 3.6 - - + -
208D VAL 4.7 0.2 - - - -
209D ALA* 3.5 3.2 - - - +
210D HIS* 3.0 36.0 + - - +
211D PRO* 5.3 0.2 - - - +
213D SER* 2.7 33.4 + - - -
214D SER* 1.4 74.4 - - - +
216D LYS* 1.3 70.0 + - - +
217D VAL* 3.7 18.8 - - + -
708D GOL 3.6 29.2 + - - +
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Residues in contact with LYS 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D VAL 3.4 6.1 - - - +
209D ALA* 4.2 17.0 - - + -
214D SER 4.4 0.4 + - - -
215D THR* 1.3 80.5 - - - +
217D VAL* 1.3 64.4 + - - +
218D ASP* 5.1 4.3 - - - +
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PRO* 4.9 3.6 - - + +
132D VAL* 3.9 39.0 - - + +
206D CYS 3.8 0.9 - - - +
208D VAL* 2.8 38.7 + - + +
215D THR* 3.7 20.4 - - + -
216D LYS* 1.3 77.5 - - - +
218D ASP* 1.3 75.4 + - - +
219D LYS* 4.2 3.6 - - + -
619D EDO 4.5 13.9 - - - +
708D GOL 4.4 14.8 - - - +
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Residues in contact with ASP 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D SER* 5.3 1.6 + - - -
205D THR* 4.2 9.5 - - + +
206D CYS 3.4 3.6 - - - -
207D ASN* 3.1 31.1 + - - +
216D LYS* 5.1 4.3 - - - +
217D VAL* 1.3 85.7 + - - +
219D LYS* 1.3 62.4 + - - +
220D LYS 4.2 0.9 + - - -
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Residues in contact with LYS 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLU* 3.2 32.1 + - - +
132D VAL* 3.5 26.9 - - + +
134D PRO* 4.1 25.1 - - + -
205D THR* 3.3 4.2 - - - +
206D CYS* 2.9 49.7 + - - -
217D VAL* 4.2 2.2 - - + -
218D ASP* 1.3 75.1 - - - +
220D LYS* 1.3 68.4 + - - +
221D ILE* 3.6 5.2 + - - +
619D EDO 2.7 34.4 + - - +
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Residues in contact with LYS 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PRO* 4.4 4.7 - - - +
202D GLU 5.6 0.7 - - - -
203D THR* 3.6 31.2 + - + +
204D VAL 4.1 3.4 - - - +
205D THR* 3.6 22.5 - - + +
218D ASP 4.2 1.0 + - - -
219D LYS* 1.3 81.4 - - - +
221D ILE* 1.3 68.0 + - - +
222D VAL* 3.3 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