Contacts of the helix formed by residues 196 - 211 (chain A) in PDB entry 1UZF
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 PHE 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ILE* 3.8 26.9 - - + +
141A ASP* 3.6 35.7 - - + -
142A MET* 3.4 30.5 - - + -
145A THR* 4.0 18.2 - - + -
192A ALA 3.5 20.0 - - - -
193A ILE* 2.9 8.0 + - - +
195A GLN* 1.3 112.0 - - - +
197A TYR* 1.3 64.2 + - - +
198A PRO* 3.6 1.8 - - - -
199A LYS* 3.5 6.2 + - - +
200A TYR* 3.1 21.0 + - - +
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Residues in contact with TYR 197 (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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142A MET* 4.2 12.3 - - - -
193A ILE* 3.3 5.6 + - + +
194A LEU 4.2 3.6 - - - +
196A PHE* 1.3 74.1 - - - +
198A PRO* 1.3 74.6 - - + +
200A TYR* 3.1 32.9 + + - +
201A VAL* 2.8 50.3 + - + +
467A TRP* 3.8 18.6 - + - -
468A ARG* 3.6 29.8 - - - +
471A VAL* 4.3 5.2 - - + -
472A PHE* 4.9 1.0 - - - -
481A TYR* 3.9 14.6 - + + -
506A PHE* 3.5 32.1 - + + -
514A ILE* 3.3 36.0 + - + +
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Residues in contact with PRO 198 (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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194A LEU* 3.2 24.0 - - + +
195A GLN 4.5 3.8 - - - +
196A PHE 3.8 2.0 - - - -
197A TYR* 1.3 87.7 - - + +
199A LYS* 1.3 56.7 + - - +
201A VAL* 3.3 4.6 + - + +
202A GLU* 3.0 27.2 + - - +
478A LYS* 3.9 30.7 - - + +
481A TYR* 3.5 25.6 - - + +
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Residues in contact with LYS 199 (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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134A GLU* 3.4 39.4 + - - +
138A ILE* 4.6 14.4 - - + -
195A GLN 5.4 3.5 + - - +
196A PHE* 3.5 8.6 + - - +
197A TYR 3.3 0.8 - - - -
198A PRO* 1.3 76.1 - - - +
200A TYR* 1.3 66.9 + - - +
202A GLU* 2.6 36.0 + - - +
203A LEU* 2.9 42.5 + - + +
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Residues in contact with TYR 200 (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 TYR* 3.9 14.9 - + - -
138A ILE* 3.9 17.0 - - + +
139A LEU* 4.0 7.6 - - + -
142A MET* 3.8 16.2 - - + -
196A PHE 3.1 14.4 + - - +
197A TYR* 3.1 53.5 + + - +
199A LYS* 1.3 77.9 - - - +
201A VAL* 1.3 67.1 + - + +
203A LEU* 3.3 4.0 + - - +
204A ILE* 2.9 55.9 + - + +
220A TRP* 3.8 5.5 - - - -
468A ARG* 4.9 0.3 + - - -
472A PHE* 3.7 21.9 - + - -
514A ILE 4.6 1.0 + - - -
517A SER* 2.8 41.5 + - - -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 2.8 35.6 + - + +
198A PRO* 3.6 9.2 - - + +
200A TYR* 1.3 80.8 - - + +
202A GLU* 1.3 65.0 + - - +
204A ILE* 3.8 7.6 - - - -
205A ASN* 3.1 41.9 + - - +
471A VAL* 3.6 38.6 - - + +
472A PHE* 4.3 7.0 - - + -
481A TYR* 4.1 5.2 - - - +
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Residues in contact with GLU 202 (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 PRO 3.0 12.7 + - - +
199A LYS* 2.6 47.2 + - - +
201A VAL* 1.3 78.7 - - - +
203A LEU* 1.3 63.1 + - + +
205A ASN* 3.8 4.4 - - - +
206A GLN* 3.0 30.9 + - + +
209A ARG* 4.8 3.1 + - - +
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Residues in contact with LEU 203 (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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127A LEU* 3.7 6.3 - - + +
131A GLU* 3.9 33.7 - - + +
134A GLU* 3.9 23.3 - - + +
135A TYR* 3.6 52.0 - - + +
138A ILE* 4.6 3.4 - - + -
199A LYS* 2.9 33.4 + - + +
200A TYR 4.0 0.2 - - - +
202A GLU* 1.3 79.5 - - + +
204A ILE* 1.3 65.5 + - - +
206A GLN* 3.3 14.1 + - - +
207A ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 204 (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 TYR* 3.4 31.6 - - + +
200A TYR* 2.9 47.6 + - + +
201A VAL* 3.4 8.5 - - - +
203A LEU* 1.3 73.4 - - - +
205A ASN* 1.3 62.0 + - - +
207A ALA* 3.6 6.3 + - + +
208A ALA* 3.0 25.3 + - - +
216A ALA* 3.8 13.7 - - + -
220A TRP* 3.9 25.8 - - + +
472A PHE* 3.7 24.0 - - + -
517A SER* 4.0 2.5 - - - +
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Residues in contact with ASN 205 (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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201A VAL* 3.1 37.3 + - - +
202A GLU* 3.8 3.8 - - - +
204A ILE* 1.3 78.3 - - - +
206A GLN* 1.3 59.6 + - - +
208A ALA* 3.0 8.0 + - - +
209A ARG* 2.8 46.1 + - - +
215A ASP* 3.5 8.4 - - - +
216A ALA* 2.8 36.1 + - - +
471A VAL 4.6 0.2 + - - -
472A PHE* 2.9 29.2 + - - +
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Residues in contact with GLN 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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127A LEU* 3.8 8.2 - - + +
128A PRO* 3.8 21.2 - - - +
131A GLU* 3.7 22.4 + - - +
202A GLU* 3.0 21.7 + - + +
203A LEU* 3.3 24.7 + - - +
205A ASN* 1.3 77.0 - - - +
207A ALA* 1.3 62.4 + - - +
209A ARG* 3.1 29.4 + - - +
210A LEU* 2.9 38.4 + - + +
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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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123A GLU 4.0 16.6 - - - +
124A ARG* 4.2 8.1 - - + -
126A ALA* 5.0 0.7 - - - -
127A LEU* 3.5 24.8 - - + +
135A TYR* 5.8 1.3 - - + -
203A LEU 3.0 16.5 + - - +
204A ILE* 3.7 9.0 - - + +
206A GLN* 1.3 75.3 - - - +
208A ALA* 1.3 62.7 + - - +
210A LEU* 3.2 14.8 + - - +
211A ASN* 2.9 23.5 + - - +
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Residues in contact with ALA 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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204A ILE 3.0 12.1 + - - +
205A ASN 3.0 10.0 + - - +
207A ALA* 1.3 76.9 - - - +
209A ARG* 1.3 61.4 + - - +
211A ASN* 3.0 16.4 + - - +
212A GLY 3.4 0.3 + - - -
213A TYR* 3.0 26.8 + - + +
215A ASP 3.3 34.1 - - - +
216A ALA* 3.4 8.3 - - - +
219A SER* 4.3 7.4 - - - -
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Residues in contact with ARG 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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202A GLU* 4.8 2.0 + - - +
205A ASN* 2.8 37.1 + - - +
206A GLN* 3.5 37.0 - - - +
208A ALA* 1.3 73.3 - - - +
210A LEU* 1.3 63.3 + - + +
211A ASN 3.1 0.9 + - - -
212A GLY* 3.2 12.3 + - - -
213A TYR 3.1 12.0 - - - +
214A VAL* 3.7 25.0 + - - +
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Residues in contact with LEU 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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100A ARG* 3.5 19.2 + - - -
126A ALA* 3.4 37.9 - - + +
127A LEU* 4.1 11.4 - - + -
128A PRO* 4.2 4.5 - - + -
206A GLN* 2.9 42.2 + - + +
207A ALA* 3.2 6.7 + - - +
209A ARG* 1.3 78.6 - - + +
211A ASN* 1.3 59.7 + - - +
212A GLY 3.4 0.2 - - - -
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Residues in contact with ASN 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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100A ARG* 3.1 18.1 + - - +
120A GLN 5.6 0.5 - - - +
121A ASP* 3.2 23.8 + - - +
122A LEU* 2.8 24.3 + - - +
123A GLU* 2.9 34.4 + - - +
126A ALA* 3.6 3.0 - - - +
207A ALA 2.9 20.2 + - - -
208A ALA* 3.0 10.3 + - - +
210A LEU* 1.3 80.4 - - - +
212A GLY* 1.3 58.1 + - - +
213A TYR* 3.5 19.4 - - + -
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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