Contacts of the strand formed by residues 212 - 217 (chain C) in PDB entry 2ZA5
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 212 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 3.9 24.9 - - + +
30C GLN* 3.3 26.7 - - - +
46C GLY 3.9 6.7 - - - +
47C SER* 3.9 8.5 - - - -
141C TRP 3.8 1.2 - - - +
142C VAL* 3.6 21.0 - - - +
143C THR* 3.6 10.8 + - - +
211C GLY* 1.3 84.9 - - - +
213C LEU* 1.3 59.7 + - - +
214C VAL* 3.8 17.3 + - + +
223C GLN* 3.7 23.3 - - - +
225C GLY 3.7 5.4 - - - +
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C CYS* 3.9 13.7 - - + -
141C TRP 3.4 17.0 - - - +
142C VAL* 4.0 6.7 - - + +
165C VAL* 3.7 28.0 - - + -
167C ILE* 4.4 6.7 - - + -
195C LEU* 3.5 32.5 - - + -
197C ALA* 4.1 7.4 - - + -
211C GLY 3.8 1.0 + - - -
212C PRO* 1.3 70.9 - - - +
214C VAL* 1.3 60.2 + - - +
223C GLN* 3.6 3.1 - - - -
224C ALA* 2.9 28.9 + - + -
225C GLY 2.9 20.3 + - - +
242C TYR* 3.6 30.2 - - + -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TRP* 3.7 24.7 - - + -
29C TRP* 4.0 16.6 - - + +
125C VAL* 4.2 8.1 - - + -
140C CYS* 3.1 2.6 - - - +
141C TRP* 2.7 49.2 + - + +
143C THR* 6.1 1.3 - - + +
212C PRO* 3.8 20.8 - - + +
213C LEU* 1.3 79.7 - - - +
215C CYS* 1.3 61.5 + - - +
221C TRP* 3.5 24.8 - - + -
222C LEU 3.3 7.9 - - - +
223C GLN* 3.9 17.3 - - + -
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Residues in contact with CYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.9 32.1 - - + -
138C MET* 4.1 8.1 - - - -
139C PRO 3.3 6.7 - - - +
140C CYS* 2.0 45.8 - - - -
167C ILE* 4.7 1.8 - - - -
213C LEU* 4.9 1.6 - - - -
214C VAL* 1.3 75.4 - - - +
216C LYS* 1.3 62.7 + - - +
217C VAL* 3.7 1.0 + - + -
220C THR 3.5 0.5 - - - +
221C TRP* 3.5 5.3 - - - -
222C LEU* 2.8 32.6 + - - +
224C ALA* 3.9 13.9 - - - -
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Residues in contact with LYS 216 (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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138C MET* 4.4 9.4 - - - +
139C PRO* 3.3 26.2 + - + +
215C CYS* 1.3 72.9 - - - +
217C VAL* 1.3 63.0 + - - +
219C GLY* 3.7 38.8 - - - +
220C THR 3.5 6.1 - - - +
221C TRP* 3.7 45.9 - - + +
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Residues in contact with VAL 217 (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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132C GLU* 4.0 21.8 - - - +
134C PHE* 4.3 16.8 - - + -
138C MET* 4.3 16.4 - - + -
215C CYS 4.1 5.6 - - - +
216C LYS* 1.3 75.5 - - - +
218C ASN* 1.3 81.8 + - + +
219C GLY 3.2 0.4 - - - -
220C THR* 2.9 29.3 + - - +
222C LEU* 3.2 29.7 - - + +
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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