Contacts of the helix formed by residues 188 - 200 (chain A) in PDB entry 2X1L
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A ILE 4.0 1.4 - - - +
187A GLY* 1.3 88.3 - - - +
189A ASP* 1.3 66.8 + - - +
190A ALA* 4.6 4.5 - - + +
191A ARG* 3.0 36.0 + - + +
192A ARG 3.4 4.0 + - - -
290A PHE* 3.5 20.8 - - + -
291A ALA 3.4 21.3 - - - +
334A PHE 5.9 0.2 - - - +
335A GLY* 4.5 15.0 - - - +
603A 2HP 3.4 18.6 - - - +
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Residues in contact with ASP 189 (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 PRO* 1.3 71.6 - - - +
190A ALA* 1.3 62.1 + - - +
192A ARG* 2.7 56.2 + - - +
193A ASN* 3.1 22.6 + - - +
603A 2HP 2.7 35.2 + - - +
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Residues in contact with ALA 190 (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 PRO* 3.3 5.3 - - + +
189A ASP* 1.3 77.2 - - - +
191A ARG* 1.3 82.1 + - - +
193A ASN* 3.5 13.7 + - - +
194A GLU* 3.3 27.5 + - - +
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Residues in contact with ARG 191 (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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186A ILE* 4.1 5.6 - - + -
187A GLY 4.3 1.6 - - - +
188A PRO* 3.0 35.6 + - + +
190A ALA* 1.3 88.5 - - - +
192A ARG* 1.3 64.0 + - - +
194A GLU* 2.7 47.3 + - - +
195A ILE* 3.1 26.0 + - - +
264A LYS* 4.0 45.0 - - - +
267A ILE* 3.5 27.3 - - + +
291A ALA* 4.2 5.2 - - + -
335A GLY 4.2 16.6 + - - -
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Residues in contact with ARG 192 (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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179A TYR* 4.3 12.9 + - + +
182A HIS 5.2 0.2 - - - -
183A PRO* 3.0 53.1 + - - +
186A ILE* 3.6 45.8 + - + +
188A PRO 3.4 2.6 + - - -
189A ASP* 2.7 46.9 + - - +
191A ARG* 1.3 75.8 - - - +
193A ASN* 1.3 70.3 + - - +
195A ILE* 3.1 2.1 + - - +
196A VAL* 2.8 45.4 + - + +
603A 2HP 5.4 0.2 + - - -
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Residues in contact with ASN 193 (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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189A ASP* 3.1 23.5 + - - +
190A ALA* 3.7 11.7 - - - +
191A ARG 3.3 0.2 - - - -
192A ARG* 1.3 88.6 + - - +
194A GLU* 1.3 56.5 + - + +
196A VAL* 3.6 7.3 + - - +
197A SER* 3.1 28.1 + - - -
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Residues in contact with GLU 194 (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* 3.3 16.2 + - - +
191A ARG* 2.7 48.4 + - - +
192A ARG 3.2 0.8 - - - -
193A ASN* 1.3 76.3 - - + +
195A ILE* 1.3 62.6 + - + +
197A SER* 3.5 6.2 + - - -
198A PHE* 3.0 29.0 + - - +
267A ILE* 6.0 1.9 - - - +
268A ARG* 5.6 0.9 + - - -
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Residues in contact with ILE 195 (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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179A TYR* 3.6 32.3 - - + +
186A ILE* 3.8 13.9 - - + -
191A ARG 3.1 14.6 + - - +
192A ARG 3.1 6.2 + - - +
194A GLU* 1.3 76.9 - - + +
196A VAL* 1.3 60.4 + - - +
198A PHE* 3.2 4.2 + - + +
199A VAL* 2.9 35.2 + - - +
267A ILE* 3.9 22.2 - - + -
268A ARG* 3.8 29.8 - - + +
271A THR* 3.4 26.0 - - - +
272A VAL* 4.0 8.5 - - + -
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Residues in contact with VAL 196 (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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176A LEU* 4.0 8.8 - - + +
179A TYR* 3.9 36.6 - - + -
192A ARG* 2.8 30.3 + - + +
193A ASN* 3.8 8.3 - - - +
195A ILE* 1.3 76.8 - - - +
197A SER* 1.3 54.0 + - - +
199A VAL 3.5 0.3 + - - -
200A SER* 2.7 45.6 + - - +
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Residues in contact with SER 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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193A ASN 3.1 19.0 + - - -
194A GLU* 3.7 7.9 - - - -
196A VAL* 1.3 77.8 - - - +
198A PHE* 1.3 62.2 + - - +
200A SER* 3.7 6.8 + - - -
201A GLY* 3.7 12.6 + - - -
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Residues in contact with PHE 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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138A GLU* 5.5 5.6 - - - -
194A GLU 3.0 17.7 + - - +
195A ILE* 3.2 5.6 + - + +
197A SER* 1.3 75.2 - - - +
199A VAL* 1.3 74.6 + - + +
201A GLY* 3.4 12.5 + - - -
202A GLY 4.3 7.7 + - - +
203A LEU* 3.7 25.7 - - + +
268A ARG* 3.4 59.5 - - + +
272A VAL* 4.3 15.3 - - + -
273A TYR* 5.3 9.9 - + - -
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Residues in contact with VAL 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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172A THR* 3.6 41.2 - - + +
175A LEU* 4.5 2.5 - - + -
176A LEU* 3.8 18.2 - - + -
179A TYR* 3.7 27.6 - - + +
195A ILE 2.9 21.0 + - - +
198A PHE* 1.3 75.3 - - + +
200A SER* 1.3 57.2 + - - +
201A GLY 3.1 5.2 - - - -
202A GLY* 3.0 18.7 + - - -
203A LEU* 3.9 16.2 - - + -
272A VAL* 3.9 22.9 - - + -
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Residues in contact with SER 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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172A THR* 5.9 0.2 - - - -
176A LEU* 3.6 22.6 - - - +
196A VAL* 2.7 28.6 + - - +
197A SER* 3.9 8.7 - - - -
198A PHE 3.3 0.4 - - - -
199A VAL* 1.3 75.7 - - - +
201A GLY* 1.3 58.0 + - - +
202A GLY 3.2 2.0 + - - -
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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