Contacts of the strand formed by residues 214 - 221 (chain A) in PDB entry 5ZF6
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 LEU 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ARG* 5.8 0.2 - - - +
193A ILE* 3.9 6.3 - - + +
194A GLY* 3.2 12.5 - - - -
195A ILE* 3.9 24.0 - - + +
204A PRO* 5.8 0.2 - - - +
209A MET* 5.9 0.9 - - - +
212A SER* 2.6 26.0 + - - -
213A THR* 1.3 81.6 + - - +
215A ASN* 1.3 65.2 + - - +
216A LEU* 3.8 22.2 - - + +
231A ALA* 4.3 1.6 - - + -
232A SER 3.6 13.9 - - - +
233A ALA* 3.8 6.5 - - + -
236A ILE* 4.0 12.1 - - + -
241A PHE* 3.6 31.6 - - + -
244A ALA* 3.5 32.8 - - + -
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Residues in contact with ASN 215 (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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192A ARG* 2.7 43.3 + - - +
193A ILE 4.0 0.9 - - - -
209A MET* 3.7 19.3 - - + +
212A SER* 6.4 0.2 - - - -
214A LEU* 1.3 72.3 - - - +
216A LEU* 1.3 57.9 + - - +
217A VAL* 3.9 5.9 - - - +
230A GLU 3.7 1.6 - - - +
231A ALA* 3.2 4.5 - - - -
232A SER* 2.8 45.3 + - - +
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Residues in contact with LEU 216 (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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192A ARG* 3.1 5.4 - - - +
193A ILE* 2.6 61.5 + - + +
214A LEU* 3.8 22.0 - - + -
215A ASN* 1.3 73.3 + - - +
217A VAL* 1.3 64.1 + - - +
218A VAL* 3.9 25.1 - - + -
229A LEU* 3.7 24.7 - - + -
230A GLU 3.7 2.9 - - - +
231A ALA* 3.5 20.9 - - + -
241A PHE* 4.5 7.9 - - + -
244A ALA* 4.3 11.7 - - + +
245A ILE* 4.6 13.9 - - + -
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Residues in contact with VAL 217 (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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133A ILE* 4.3 12.6 - - + -
167A VAL* 4.3 7.4 - - + -
170A ILE* 4.1 19.3 - - + -
190A ALA* 5.4 0.7 - - + -
191A VAL 3.5 8.7 - - - +
192A ARG* 3.6 34.8 - - + +
215A ASN* 3.9 7.4 - - - +
216A LEU* 1.3 77.6 - - - +
218A VAL* 1.3 63.1 + - - +
228A MET* 3.6 21.5 - - + +
229A LEU* 3.6 5.2 - - - +
230A GLU* 2.8 43.4 + - + +
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Residues in contact with VAL 218 (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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190A ALA* 3.1 4.9 - - - +
191A VAL* 3.1 40.4 + - + +
216A LEU* 3.9 12.8 - - + -
217A VAL* 1.3 74.8 - - - +
219A ALA* 1.3 69.5 + - - +
220A GLY 4.2 0.2 - - - -
226A ILE* 4.4 6.3 - - + -
228A MET* 3.4 8.5 - - - +
229A LEU* 3.9 19.5 - - + -
245A ILE* 5.1 2.2 - - + +
248A GLY* 3.7 32.3 - - - +
249A VAL* 3.9 26.0 - - + +
252A THR* 3.8 3.0 - - + +
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Residues in contact with ALA 219 (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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137A SER* 3.6 28.7 - - - +
188A VAL* 4.0 6.1 - - + -
189A GLY 3.2 9.0 - - - +
190A ALA* 4.0 6.5 - - + -
218A VAL* 1.3 77.9 - - - +
220A GLY* 1.3 59.1 + - - +
226A ILE* 3.8 4.0 - - - -
227A VAL* 3.0 40.6 + - + -
228A MET* 3.0 17.4 + - + +
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Residues in contact with GLY 220 (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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188A VAL* 3.4 7.4 - - - -
189A GLY 2.6 35.3 + - - -
218A VAL* 5.3 1.3 - - - -
219A ALA* 1.3 74.3 - - - +
221A ALA* 1.3 62.7 + - - -
225A GLN 3.2 8.7 - - - -
226A ILE* 4.7 0.7 - - - -
227A VAL* 4.8 0.4 - - - -
249A VAL* 5.8 2.7 - - - -
252A THR* 3.6 19.4 - - - +
253A GLN* 4.3 0.9 - - - -
256A ILE* 3.2 9.7 - - - +
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Residues in contact with ALA 221 (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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141A LEU* 4.9 9.0 - - + -
185A ASN 5.9 0.2 - - - +
187A PRO 4.3 2.7 - - - -
188A VAL* 4.6 1.3 - - - -
220A GLY* 1.3 73.8 - - - -
222A PRO* 1.3 79.4 - - + +
225A GLN* 2.6 29.9 + - + +
227A VAL* 3.7 24.2 - - + +
253A GLN* 3.2 15.6 + - - -
256A ILE* 3.6 2.2 - - - -
564A PRO 4.0 11.0 - - - +
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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