Contacts of the strand formed by residues 208 - 212 (chain A) in PDB entry 4DJH
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 ILE 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASN 4.5 0.5 - - - +
123A SER* 3.4 16.6 - - - +
124A TRP* 3.0 44.8 + - + +
199A THR* 3.0 37.0 - - + -
200A LYS 3.7 7.2 - - - +
201A VAL* 4.5 18.4 - - + -
206A ASP 3.2 20.6 - - - +
207A VAL* 1.3 79.1 - - - +
209A GLU* 1.3 62.9 + - - +
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Residues in contact with GLU 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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198A GLY 3.7 0.7 - - - +
199A THR* 3.4 10.6 - - - +
200A LYS* 3.0 36.6 + - + +
202A ARG* 3.5 50.9 + - + +
207A VAL* 4.7 2.5 - - + -
208A ILE* 1.3 74.8 - - - +
210A CYS* 1.3 63.9 + - - +
211A SER* 4.1 5.7 + - - -
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Residues in contact with CYS 210 (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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124A TRP* 3.3 40.2 - - + +
131A CYS* 2.0 64.4 - - - -
135A LEU* 4.2 0.9 - - - -
198A GLY 3.8 0.4 - - - -
199A THR* 4.8 0.9 - - - -
209A GLU* 1.3 73.0 - - - +
211A SER* 1.3 65.6 + - - +
1300A JDC 3.8 28.8 + - + -
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Residues in contact with SER 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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135A LEU* 3.8 15.9 - - - -
198A GLY* 3.0 32.1 + - - +
209A GLU* 4.1 8.0 - - - -
210A CYS* 1.3 80.0 - - - +
212A LEU* 1.3 74.1 + - - +
213A GLN* 3.6 3.2 + - - +
219A TYR* 3.3 22.7 + - - -
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Residues in contact with LEU 212 (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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135A LEU* 3.9 23.7 - - + +
139A TYR* 3.6 31.6 - - + +
192A SER 4.7 0.2 - - - +
193A ALA* 3.9 22.9 - - + -
196A LEU* 3.5 25.1 - - + -
197A GLY 3.9 2.2 - - - +
211A SER* 1.3 81.4 + - - +
213A GLN* 1.3 59.9 + - - +
214A PHE* 3.8 19.7 - - + -
219A TYR* 3.1 26.1 - - - +
223A ASP* 6.1 0.4 - - - +
226A MET* 3.7 24.0 - - - -
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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