Contacts of the strand formed by residues 205 - 209 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C GLN* 3.2 6.2 - - - -
160C THR* 2.8 44.4 + - - +
162C ALA 5.3 0.7 - - - -
164C ILE* 4.3 12.6 - - - -
186C ALA 3.8 4.9 - - - -
187C ILE* 4.1 10.5 - - - -
203C GLY 3.8 0.4 - - - -
204C LEU* 1.3 72.7 - - - +
206C PHE* 1.3 66.0 + - - -
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Residues in contact with PHE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.1 26.5 - - + -
140C ARG* 3.8 12.3 - - + -
142C VAL* 3.7 37.0 - - + -
155C LEU* 5.0 2.9 - - + -
157C ALA* 3.8 15.9 - - + -
158C ILE 3.3 1.8 - - - -
159C GLN* 3.5 37.9 - - + -
160C THR* 5.5 0.4 - - - -
164C ILE* 4.8 3.1 - - - +
184C ASN* 3.8 4.0 - - - +
185C SER* 2.9 24.3 + - - -
186C ALA* 2.7 29.4 + - + +
187C ILE* 4.0 2.7 - - - -
188C ALA* 3.6 32.1 - - + -
204C LEU 4.0 3.8 - - - -
205C GLY* 1.3 78.8 - - - -
207C ALA* 1.3 60.8 + - - +
408F VAL* 4.6 5.8 - - + -
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LEU* 5.4 0.7 - - - -
157C ALA* 3.2 9.1 - - - -
158C ILE* 2.8 37.7 + - + +
160C THR* 5.6 0.9 - - + -
173C LEU* 4.0 20.4 - - + -
182C GLY* 4.2 3.1 - - - -
183C VAL 3.1 25.6 - - - +
184C ASN* 3.8 14.8 - - - +
185C SER* 5.1 0.7 - - - -
206C PHE* 1.3 74.6 - - - +
208C ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASN* 3.9 10.8 - - - +
87C SER* 3.2 27.4 - - - +
88C ASP* 4.0 2.5 - - + +
89C ILE* 3.9 14.1 - - + -
155C LEU* 4.0 28.5 - - + -
157C ALA* 5.1 0.7 - - - +
182C GLY* 3.1 1.8 - - - -
183C VAL* 2.8 43.4 + - + +
185C SER* 3.3 19.7 + - - +
207C ALA* 1.3 70.8 - - - +
209C PRO* 1.3 81.3 - - + +
210C VAL* 4.4 0.2 - - - -
212C GLN* 4.2 10.8 - - + +
213C ALA* 4.1 18.4 - - + +
216C ILE* 6.4 0.7 - - + -
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Residues in contact with PRO 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C SER* 3.5 21.5 - - - +
139C ASN* 5.5 4.0 - - - +
156C ASP* 3.2 30.1 - - - +
158C ILE* 3.6 24.5 - - + -
207C ALA 3.5 4.4 - - - +
208C ILE* 1.3 91.0 - - + +
210C VAL* 1.3 66.9 + - - +
211C ASP* 4.5 1.1 - - + +
212C GLN* 3.1 28.6 + - - +
213C ALA 3.0 18.0 + - - -
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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