Contacts of the strand formed by residues 180 - 189 (chain A) in PDB entry 1XHU
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 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLN 4.0 0.2 - - - +
20A VAL* 2.8 35.7 + - + +
21A LYS 4.1 4.0 + - - +
22A ARG* 4.6 0.4 - - - -
23A PRO* 3.5 27.6 - - + -
28A LEU* 4.1 3.8 - - + -
33A ALA 3.4 25.1 - - - +
34A GLY* 4.2 1.6 - - - -
36A PRO* 5.1 1.1 - - + -
37A PHE* 3.1 32.3 - - + -
173A TRP* 3.1 43.1 - - + -
174A GLU 3.5 2.9 - - - -
175A LEU* 3.5 23.1 - - + -
179A ASP* 1.3 70.5 - - - +
181A VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 181 (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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17A GLY* 3.9 18.4 - - - +
18A GLN 3.5 16.6 - - - +
19A LYS* 4.4 16.6 - - + +
173A TRP* 3.1 5.3 - - - +
174A GLU* 2.7 58.1 + - + +
176A ASN* 3.4 32.1 - - + +
179A ASP 3.7 3.2 + - - -
180A LEU* 1.3 76.3 - - - +
182A CYS* 1.3 78.7 + - - +
183A VAL* 4.6 2.7 - - + -
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Residues in contact with CYS 182 (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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15A LEU* 4.1 20.6 - - - +
16A ILE* 3.6 25.0 - - - +
17A GLY* 3.2 20.6 + - - -
18A GLN* 3.6 4.5 + - + +
37A PHE* 3.7 22.0 - - + -
171A VAL* 4.6 9.2 - - + -
172A ASP 3.3 15.3 - - - +
173A TRP* 3.8 2.2 - - + +
180A LEU 4.0 0.6 + - - -
181A VAL* 1.3 83.9 - - - +
183A VAL* 1.3 64.9 + - - +
184A SER 3.5 15.7 - - - -
185A THR* 4.7 2.0 - - - -
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Residues in contact with VAL 183 (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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16A ILE* 3.1 25.6 - - - +
133A ILE* 3.6 28.9 - - + -
172A ASP* 2.9 12.7 + - + +
173A TRP 4.5 0.2 - - - +
174A GLU* 3.7 37.9 - - + +
181A VAL* 4.6 3.6 - - + -
182A CYS* 1.3 77.9 - - - +
184A SER* 1.3 76.3 + - - +
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Residues in contact with SER 184 (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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16A ILE* 3.3 8.3 - - - -
133A ILE* 5.0 0.9 - - - +
172A ASP* 2.2 55.1 + - - +
182A CYS* 3.5 8.0 - - - -
183A VAL* 1.3 84.7 - - - +
185A THR* 1.3 66.4 + - - +
186A SER* 6.1 0.2 - - - -
213A ARG* 3.6 8.6 + - - -
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Residues in contact with THR 185 (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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8A TYR* 2.6 49.3 + - + +
11A ILE* 6.3 0.9 - - + -
12A ASN* 3.2 32.1 + - + +
15A LEU* 4.1 11.8 - - - +
16A ILE* 3.9 3.6 - - - +
169A LEU* 3.8 9.8 - - + +
170A GLU 3.2 11.1 + - - -
171A VAL* 3.9 13.7 - - - +
172A ASP* 4.3 2.0 - - - -
184A SER* 1.3 81.1 + - - +
186A SER* 1.3 63.1 + - - +
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Residues in contact with SER 186 (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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8A TYR* 3.2 6.3 - - - -
169A LEU* 3.3 6.1 - - - +
170A GLU* 2.6 47.3 + - - +
172A ASP* 4.9 1.9 + - - -
184A SER* 6.1 0.2 - - - -
185A THR* 1.3 78.2 + - - +
187A PHE* 1.3 60.5 - - - +
212A VAL* 3.8 2.2 - - - +
213A ARG* 3.6 45.7 + - - +
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Residues in contact with PHE 187 (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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2A SER* 3.8 11.7 - - - -
4A ILE* 3.4 23.8 - - + -
5A LYS* 3.9 28.0 - - + -
8A TYR* 3.6 30.8 + + + -
124A GLU* 4.3 0.2 - - - -
126A LEU* 4.4 6.3 - - + -
167A ASN* 3.5 37.7 - - + -
168A TYR 3.3 15.9 - - - -
169A LEU* 4.4 11.9 - - + -
186A SER* 1.3 75.6 - - - +
188A ALA* 1.3 77.7 + - - +
189A GLU* 3.9 26.0 - - + -
212A VAL* 3.7 3.4 - - - +
217A GLN* 5.4 1.4 - - - +
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Residues in contact with ALA 188 (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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167A ASN* 3.4 2.8 - - - +
168A TYR* 2.8 38.4 + - + +
187A PHE* 1.3 86.1 - - - +
189A GLU* 1.3 62.3 + - - +
212A VAL* 3.5 23.6 - - + +
215A LEU* 3.6 17.5 - - + +
217A GLN* 3.2 22.7 - - + +
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Residues in contact with GLU 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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2A SER* 4.0 17.0 + - - -
5A LYS* 4.3 13.0 + - - +
165A ASP* 3.3 15.8 - - - +
167A ASN* 3.1 26.7 + - - +
187A PHE* 3.9 18.7 - - + -
188A ALA* 1.3 75.7 - - - +
190A LEU* 1.3 66.1 + - - +
191A PHE 4.7 0.4 - - - +
192A LYS* 3.4 46.1 + - + +
193A SER 3.8 0.9 + - - -
215A LEU* 3.7 4.8 - - - +
217A GLN* 2.9 23.6 + - - +
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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