Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 5AVD
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 PRO 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A SER* 5.5 0.4 - - - +
30A GLN* 3.3 25.8 - - + +
47A GLY 3.9 3.1 - - - +
48A THR* 3.5 20.4 - - - +
143A TYR 4.1 0.3 - - - +
144A ILE* 3.8 9.2 - - - +
145A THR* 3.3 27.4 + - - +
205A GLY* 1.3 88.3 - - - +
207A LEU* 1.3 58.8 + - - +
208A HIS* 3.1 40.6 - - + +
217A VAL* 3.7 11.7 - - + -
219A GLY 3.4 6.7 - - - +
221A THR* 4.5 2.9 - - - -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A CYS* 3.7 25.8 - - + -
143A TYR 3.6 16.6 - - - +
144A ILE* 3.9 4.3 - - + +
165A LEU* 4.4 3.1 - - + +
188A VAL* 3.9 26.2 - - + -
190A ALA* 4.2 12.3 - - + -
206A PRO* 1.3 73.0 - - - +
208A HIS* 1.3 59.3 - - - +
209A CYS* 3.9 16.6 + - - -
217A VAL* 3.4 2.9 - - - -
218A HIS* 2.9 28.2 + - + +
219A GLY 3.0 17.0 + - - +
238A PHE* 3.7 44.2 - - + -
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Residues in contact with HIS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.5 54.1 - + + -
29A SER* 4.3 14.6 + - - -
30A GLN* 5.4 1.1 - - + -
142A CYS* 3.0 1.9 - - - -
143A TYR 2.8 48.4 + - - +
145A THR* 2.9 32.1 + - + -
206A PRO* 3.1 24.4 - - + +
207A LEU* 1.3 72.1 - - - +
209A CYS* 1.3 59.8 + - - +
215A TYR* 3.8 16.0 - - + +
216A ALA 3.4 7.4 - - - +
217A VAL* 3.9 13.1 - - - +
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Residues in contact with CYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.5 22.0 - - + -
140A SER* 5.8 0.7 - - - -
141A PRO 3.4 4.9 - - - +
142A CYS* 2.0 45.3 - - - -
207A LEU* 3.9 14.6 - - - -
208A HIS* 1.3 75.1 - - - +
210A LEU* 1.3 62.9 + - - +
211A VAL* 3.5 8.7 + - + +
214A GLN 3.5 1.4 - - - +
215A TYR* 3.4 4.3 - - - -
216A ALA* 2.8 29.7 + - - +
218A HIS* 3.8 22.0 - - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 6.0 0.3 - - - -
141A PRO* 3.1 38.4 + - + +
209A CYS* 1.3 69.8 - - - +
211A VAL* 1.3 63.7 + - - +
213A GLY* 3.6 38.1 - - - +
214A GLN 3.6 9.6 - - - +
215A TYR* 3.6 37.2 - - + +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A THR* 6.2 2.9 - - + -
136A LEU* 4.1 19.3 - - + -
209A CYS* 4.0 10.8 - - + +
210A LEU* 1.3 80.2 - - - +
212A ASN* 1.3 88.1 + - - +
213A GLY 3.1 1.9 + - - -
214A GLN* 2.9 26.4 + - - +
216A ALA* 5.9 2.2 - - + -
218A HIS* 4.0 20.6 - - + +
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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