Contacts of the strand formed by residues 200 - 205 (chain D) in PDB entry 3DIF
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 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D TRP* 3.2 8.6 - - - -
161D ASN* 2.7 45.4 + - - -
198D THR* 3.6 12.6 + - - -
199D VAL* 1.3 79.2 + - - +
201D CYS* 1.3 63.3 + - - +
202D ASN* 3.7 18.1 - - - +
213D ASP* 4.0 8.5 - - + +
214D LYS 3.4 26.2 - - - +
215D LYS* 3.8 10.8 - - + +
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Residues in contact with CYS 201 (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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127D VAL* 4.1 1.1 - - - -
128D TYR 5.5 0.7 - - - -
146D CYS* 2.0 48.7 - - + -
158D VAL* 4.7 3.1 - - + -
159D THR 3.6 5.4 - - - +
160D TRP* 3.5 27.1 - - + -
200D THR* 1.3 70.2 - - - +
202D ASN* 1.3 61.1 + - - +
203D VAL* 4.3 0.7 - - - +
212D VAL 3.5 2.9 - - - +
213D ASP* 3.5 1.2 - - - -
214D LYS* 2.8 60.4 + - - -
216D ILE* 4.2 7.6 - - - -
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Residues in contact with ASN 202 (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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157D THR 3.7 1.6 - - - +
158D VAL* 3.3 7.1 - - - +
159D THR* 2.7 48.0 + - - +
160D TRP 3.7 0.2 - - - -
161D ASN* 3.2 11.3 + - - +
162D SER* 2.6 42.5 + - - +
200D THR* 3.9 10.0 - - - +
201D CYS* 1.3 73.0 - - - +
203D VAL* 1.3 60.8 + - - +
204D ALA 4.2 0.2 - - - -
212D VAL 3.6 3.1 - - - +
213D ASP* 2.8 38.3 + - - +
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 4.3 11.4 - - + -
127D VAL* 3.7 44.2 - - + -
146D CYS* 4.2 9.6 - - - -
148D VAL* 4.0 19.7 - - + -
156D VAL* 3.5 24.0 - - + -
157D THR 3.6 2.9 - - - -
158D VAL* 4.5 5.4 - - + -
201D CYS 4.3 1.6 - - - +
202D ASN* 1.3 78.5 - - - +
204D ALA* 1.3 62.5 + - - +
210D THR 4.0 0.5 - - - +
211D LYS* 3.3 5.6 - - - +
212D VAL* 2.8 44.2 + - + +
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Residues in contact with ALA 204 (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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156D VAL* 3.2 9.9 - - - +
157D THR* 3.0 48.7 + - - +
202D ASN 4.2 0.2 - - - -
203D VAL* 1.3 75.0 - - - +
205D HIS* 1.3 58.9 + - - +
206D PRO* 3.5 7.8 - - + +
210D THR 3.6 5.6 - - - +
211D LYS* 4.5 16.8 - - + +
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Residues in contact with HIS 205 (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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122D THR* 4.2 0.7 - - + -
123D THR 3.1 25.5 + - - -
125D PRO* 3.5 30.6 - - + +
151D TYR* 3.8 4.0 - + + -
152D PHE 3.4 13.8 + - - -
153D PRO* 2.8 30.7 + - - +
155D PRO 3.5 13.0 - - - -
156D VAL* 3.5 11.4 - - + -
203D VAL 4.3 0.2 - - - -
204D ALA* 1.3 71.4 - - - +
206D PRO* 1.3 63.0 - - - +
207D ALA* 3.3 6.6 + - + +
208D SER* 2.8 34.7 + - - +
209D SER* 3.0 22.1 + - - -
210D THR* 2.8 20.0 + - - +
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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