Contacts of the strand formed by residues 205 - 209 (chain A) in PDB entry 2Z9I
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 GLY 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A GLN* 3.1 7.3 - - - +
160A THR* 2.7 45.7 + - - +
162A ALA 5.4 0.4 - - - -
164A ILE* 4.4 12.3 - - - -
186A ALA 3.8 6.7 - - - -
187A ILE* 4.1 8.7 - - - -
204A LEU* 1.3 73.1 - - - +
206A PHE* 1.3 64.5 + - - -
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Residues in contact with PHE 206 (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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140A ARG* 3.9 6.7 - - + -
142A VAL* 3.6 41.5 - - + -
155A LEU* 4.6 3.8 - - + -
157A ALA* 3.8 17.7 - - + -
158A ILE 3.1 3.4 - - - -
159A GLN* 3.6 33.7 - - + -
160A THR* 5.5 0.7 - - - -
164A ILE* 4.8 2.7 - - - +
184A ASN* 3.8 4.1 - - - +
185A SER* 2.9 25.2 + - - -
186A ALA* 2.8 31.3 + - + +
187A ILE* 4.0 6.7 - - - -
188A ALA* 3.6 27.6 - - + -
204A LEU 4.0 4.5 - - - -
205A GLY* 1.3 77.1 - - - -
207A ALA* 1.3 59.3 + - - +
126B LEU* 4.0 27.6 - - + -
408D VAL* 4.3 4.9 - - + -
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Residues in contact with ALA 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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155A LEU* 5.5 0.9 - - - -
157A ALA* 3.4 8.3 - - - -
158A ILE* 2.7 38.8 + - + +
160A THR* 5.5 0.9 - - + +
173A LEU* 4.0 21.1 - - + -
182A GLY* 4.0 3.4 - - - -
183A VAL 3.2 21.5 - - - +
184A ASN* 3.6 19.1 - - - +
185A SER* 4.6 0.7 - - - -
206A PHE* 1.3 75.4 - - - +
208A ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 208 (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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47A ASN* 3.8 7.9 - - - +
87A SER* 3.4 25.6 - - - +
88A ASP* 3.9 1.8 - - + +
89A ILE* 3.7 29.6 - - + -
155A LEU* 4.0 24.7 - - + -
156A ASP 5.0 0.4 - - - +
157A ALA* 5.3 0.4 - - - +
158A ILE* 4.5 0.2 - - - -
182A GLY* 3.1 1.7 - - - -
183A VAL* 2.8 38.7 + - + +
185A SER* 3.3 20.6 + - - +
207A ALA* 1.3 71.4 - - - +
209A PRO* 1.3 83.6 - - + +
210A VAL* 4.3 0.5 - - - -
212A GLN* 4.1 11.7 - - + +
213A ALA* 4.0 13.2 - - + +
216A ILE* 6.2 0.7 - - + -
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Residues in contact with PRO 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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108A SER* 3.5 21.3 - - - +
139A ASN* 5.9 1.6 - - - +
156A ASP* 3.0 31.2 - - - +
157A ALA 4.9 0.2 - - - -
158A ILE* 3.7 23.3 - - + +
181A VAL 3.8 0.2 - - - +
207A ALA 3.6 5.1 - - - +
208A ILE* 1.3 90.1 - - + +
210A VAL* 1.3 66.8 + - - +
211A ASP* 4.5 0.9 - - + +
212A GLN* 3.2 28.7 + - - +
213A ALA* 3.0 18.2 + - - +
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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