Contacts of the strand formed by residues 202 - 207 (chain D) in PDB entry 3IU3
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 VAL 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D VAL* 5.4 10.1 - - + -
191D CYS 3.8 0.7 - - - +
192D GLU* 3.6 1.1 - - - -
193D VAL* 2.7 43.7 + - + +
198D LEU* 3.8 32.5 - - + -
199D SER* 4.3 16.6 - - - +
200D SER* 3.9 0.2 - - - +
201D PRO* 1.3 73.3 - - - +
203D THR* 1.3 68.8 + - - +
204D LYS* 5.9 4.0 - - + -
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Residues in contact with THR 203 (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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190D ALA* 3.9 20.8 - - - +
191D CYS 3.3 8.4 + - - -
192D GLU* 4.5 12.4 - - - +
201D PRO 3.7 3.8 + - - +
202D VAL* 1.3 83.3 - - - +
204D LYS* 1.3 63.8 + - - +
205D SER* 4.3 3.1 + - - -
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Residues in contact with LYS 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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130C SER 5.0 1.9 + - - -
131C LYS* 3.6 24.5 - - - +
133C THR 3.8 18.8 + - - -
134C SER* 5.6 1.4 - - - +
112D VAL* 3.3 50.7 + - + +
114D ILE* 3.6 23.4 - - + +
191D CYS* 2.7 47.1 + - + +
193D VAL* 5.9 0.2 - - - +
202D VAL* 4.3 3.8 - - + -
203D THR* 1.3 72.8 + - - +
205D SER* 1.3 60.2 + - - +
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Residues in contact with SER 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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131C LYS* 3.1 27.0 + - - +
114D ILE* 4.6 2.5 - - - -
188D VAL* 4.6 12.3 - - - +
189D TYR 3.3 15.5 - - - -
190D ALA* 3.8 15.3 - - - -
203D THR* 4.2 4.6 + - - -
204D LYS* 1.3 76.5 - - - +
206D PHE* 1.3 64.1 + - - +
207D ASN* 5.2 1.9 + - - -
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Residues in contact with PHE 206 (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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131C LYS* 3.9 26.2 - - + +
114D ILE* 3.8 22.4 - - + -
116D PRO* 3.7 39.5 - - + -
129D VAL* 3.7 31.6 - - + -
183D TYR* 3.6 22.9 - - - -
187D LYS 3.8 0.2 - - - +
188D VAL* 3.8 2.1 - - - +
189D TYR* 3.1 54.4 + + + -
205D SER* 1.3 78.4 - - - +
207D ASN* 1.3 81.5 - - - +
208D ARG* 4.6 1.8 - - - -
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Residues in contact with ASN 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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131C LYS* 4.6 5.6 - - - +
187D LYS* 3.5 11.9 - - - +
188D VAL* 3.7 29.8 - - - +
205D SER* 5.2 2.1 + - - -
206D PHE* 1.3 88.1 - - - +
208D ARG* 1.3 64.2 + - - +
209D GLY 3.3 16.2 + - - +
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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