Contacts of the strand formed by residues 206 - 212 (chain D) in PDB entry 3EYF
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 TYR 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.9 31.9 - - + -
166D TRP* 4.4 7.9 - + + -
167D ASN* 3.5 11.2 - - - -
171D LEU* 3.9 19.1 - - + -
196D VAL* 3.4 43.4 - - + +
197D PRO* 4.8 9.0 + - - +
204D GLN* 3.6 42.0 + - + +
205D THR* 1.3 76.7 - - - +
207D ILE* 1.3 66.9 + - - +
222D LYS* 3.8 3.5 - - - +
223D VAL* 3.0 40.7 + - + +
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Residues in contact with ILE 207 (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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166D TRP* 3.5 8.1 - - - -
167D ASN* 2.6 47.2 + - - +
168D SER* 5.5 1.6 - - - +
205D THR* 4.3 15.3 - - + -
206D TYR* 1.3 77.0 - - - +
208D CYS* 1.3 66.3 + - - +
209D ASN* 3.4 19.9 + - - +
220D ASP* 4.2 16.2 - - + +
221D LYS 3.2 18.2 - - - +
222D LYS* 3.3 28.9 - - + +
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Residues in contact with CYS 208 (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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133D VAL* 4.0 8.1 - - - -
152D CYS* 2.0 52.9 - - + -
164D VAL* 4.2 8.5 - - + -
165D SER 3.5 4.5 - - - -
166D TRP* 3.7 20.7 - - + -
207D ILE* 1.3 74.2 - - - +
209D ASN* 1.3 61.4 + - - +
210D VAL* 4.1 3.1 - - - -
219D VAL 3.7 0.9 - - - +
220D ASP* 3.5 3.6 - - - -
221D LYS* 3.0 46.7 + - - -
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Residues in contact with ASN 209 (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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163D THR 3.6 1.2 - - - +
164D VAL* 3.2 6.6 - - - -
165D SER* 2.7 53.5 + - - +
168D SER* 2.8 40.4 + - - +
207D ILE* 3.4 21.6 + - - +
208D CYS* 1.3 71.5 - - - +
210D VAL* 1.3 61.9 + - - +
211D ASN* 4.0 1.6 + - - +
219D VAL 3.9 3.4 - - - -
220D ASP* 3.4 24.2 + - - +
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Residues in contact with VAL 210 (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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131D PRO* 4.9 6.1 - - + -
133D VAL* 3.8 37.5 - - + -
154D VAL* 3.9 33.0 - - + -
162D VAL* 4.7 5.2 - - + -
163D THR 3.5 7.9 - - - +
164D VAL* 4.5 9.9 - - + -
208D CYS* 4.1 12.3 - - - -
209D ASN* 1.3 76.1 - - - +
211D ASN* 1.3 67.7 + - - +
212D HIS 4.1 0.2 - - - -
217D THR 4.1 0.3 - - - +
218D LYS* 3.4 8.4 - - - +
219D VAL* 2.8 42.5 + - + +
220D ASP* 4.4 0.2 + - - -
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Residues in contact with ASN 211 (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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161D PRO 4.3 0.2 - - - +
162D VAL* 3.2 8.0 - - - +
163D THR* 2.9 48.8 + - - +
209D ASN* 4.0 1.2 + - - +
210D VAL* 1.3 74.8 - - - +
212D HIS* 1.3 64.1 + - - +
213D LYS* 3.7 35.1 + - + +
216D ASN* 6.2 0.2 - - - +
217D THR 3.8 6.4 + - - +
218D LYS* 3.1 38.7 + - - +
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Residues in contact with HIS 212 (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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129D LYS 3.3 19.3 - - - -
131D PRO* 3.8 21.7 - - + +
157D TYR* 3.7 4.8 - + + -
158D PHE 3.6 12.8 - - - -
159D PRO 2.5 31.1 + - - -
161D PRO 3.4 16.2 - - - -
162D VAL* 3.4 20.0 - - + -
210D VAL* 4.1 0.6 - - + -
211D ASN* 1.3 75.2 - - - +
213D LYS* 1.3 61.9 + - - +
214D PRO* 3.4 6.4 - - + +
215D SER* 2.4 46.5 + - - -
217D THR* 2.8 29.7 + - - +
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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