Contacts of the strand formed by residues 164 - 174 (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 PHE 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A THR* 3.4 24.9 - - + -
85A LEU* 4.8 10.3 - - + -
88A LEU* 3.8 20.2 - - + -
122A PHE* 3.8 5.4 - - - -
123A TYR* 3.1 20.4 - - + +
125A LEU* 4.4 9.9 - - + -
151A THR* 3.4 26.5 - - + -
155A MET* 4.0 27.6 - - + -
160A GLU 4.7 2.9 - - - -
163A LEU* 1.3 92.8 + - + +
165A ASP* 1.3 67.0 + - - +
166A ILE* 3.9 17.9 - - + -
191A PHE* 3.6 22.4 - + - -
223A ARG* 3.1 21.1 + - - -
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Residues in contact with ASP 165 (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 5.5 4.7 - - - +
122A PHE* 3.4 25.5 - - + -
123A TYR 2.9 11.2 + - - +
124A GLU* 3.6 4.6 - - + +
125A LEU* 2.8 33.4 + - - +
164A PHE* 1.3 72.9 - - - +
166A ILE* 1.3 63.6 + - - +
167A ASN* 3.3 15.9 + - - +
189A GLU* 3.3 25.9 - - - +
191A PHE* 4.1 8.4 - - - +
223A ARG* 2.9 28.7 + - - -
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Residues in contact with ILE 166 (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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88A LEU* 4.9 3.8 - - + -
112A THR* 5.5 2.0 - - + -
125A LEU* 3.7 35.0 - - + +
127A ASP* 6.0 0.7 - - + -
143A ILE* 4.4 14.6 - - + -
148A LEU* 5.6 2.7 - - + -
151A THR* 6.2 0.2 - - + -
164A PHE* 3.9 15.7 - - + -
165A ASP* 1.3 72.3 + - - +
167A ASN* 1.3 59.4 + - - +
168A TYR* 3.2 36.0 - - + +
190A LEU* 2.6 52.1 + - + +
191A PHE* 3.5 28.3 + - + -
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Residues in contact with ASN 167 (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* 3.7 13.7 - - - +
124A GLU* 2.3 47.5 + - - +
125A LEU 3.0 11.0 + - - +
126A LEU* 3.5 5.5 - - + +
127A ASP* 3.1 25.1 + - - +
165A ASP* 3.3 10.9 + - - +
166A ILE* 1.3 82.6 - - - +
168A TYR* 1.3 66.0 + - - +
187A PHE* 3.5 25.5 - - + -
188A ALA 3.4 3.4 - - - +
189A GLU* 3.1 24.5 + - - +
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Residues in contact with TYR 168 (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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126A LEU* 4.6 0.2 - - - -
127A ASP* 3.4 34.3 - - + +
129A LYS* 3.6 24.7 - - + -
142A ILE* 3.6 16.5 + - + -
143A ILE* 3.4 26.5 - - - +
166A ILE* 3.2 32.2 - - + +
167A ASN* 1.3 75.3 - - - +
169A LEU* 1.3 59.6 + - - +
170A GLU 4.0 0.4 - - - -
187A PHE* 3.3 7.5 - - - -
188A ALA* 2.8 42.1 + - + +
190A LEU* 3.8 24.7 - - + -
210A PHE* 3.8 18.4 - + + -
212A VAL* 3.4 23.3 - - + +
215A LEU* 5.3 0.7 - - + -
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Residues in contact with LEU 169 (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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4A ILE* 5.2 4.7 - - + -
8A TYR* 3.8 26.7 - - + -
11A ILE* 4.8 10.8 - - + -
15A LEU* 5.3 0.9 - - + -
41A VAL* 3.5 39.5 - - + -
126A LEU* 4.0 21.5 - - + +
127A ASP 3.1 8.2 + - - +
128A VAL* 3.2 13.4 - - + +
129A LYS 3.0 21.4 + - - -
168A TYR* 1.3 71.4 - - - +
170A GLU* 1.3 63.0 + - - +
171A VAL* 3.8 7.5 + - + +
185A THR* 3.8 11.4 - - + +
186A SER 3.3 14.8 - - - +
187A PHE* 4.4 7.2 - - + -
212A VAL* 4.5 1.1 - - - -
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Residues in contact with GLU 170 (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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129A LYS* 3.4 13.7 - - + +
131A ARG* 3.6 28.5 + - + -
169A LEU* 1.3 71.5 - - - +
171A VAL* 1.3 65.0 + - - +
172A ASP* 2.7 31.0 - - - +
185A THR* 3.2 11.6 + - - +
186A SER* 2.6 39.0 + - - +
211A HIS* 3.7 6.9 - - - +
212A VAL* 3.1 30.9 + - + +
213A ARG* 3.1 34.7 + - - +
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Residues in contact with VAL 171 (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* 3.5 30.3 - - + -
37A PHE* 3.7 40.6 - - + -
41A VAL* 4.4 11.0 - - + -
128A VAL* 5.7 4.7 - - + -
129A LYS 2.7 13.8 + - - +
130A THR* 3.0 12.2 - - + -
131A ARG 2.8 27.5 + - - -
169A LEU* 3.8 10.3 + - + +
170A GLU* 1.3 75.3 - - - +
172A ASP* 1.3 62.3 + - - +
173A TRP* 3.8 1.1 - - + -
182A CYS* 4.6 4.7 - - - -
184A SER 4.0 2.2 - - - -
185A THR* 3.9 4.9 - - - +
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Residues in contact with ASP 172 (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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131A ARG* 3.3 17.9 - - - +
133A ILE* 4.3 7.2 - - + -
170A GLU* 2.7 29.9 - - - +
171A VAL* 1.3 70.9 - - - +
173A TRP* 1.3 59.0 + - - +
182A CYS* 3.3 9.7 - - - -
183A VAL* 2.9 29.4 + - + -
184A SER* 2.2 47.8 + - - +
185A THR* 3.8 4.9 + - - -
186A SER* 4.9 1.2 + - - -
213A ARG* 2.9 20.2 + - - -
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Residues in contact with TRP 173 (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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28A LEU* 4.1 17.7 - - + -
33A ALA* 4.2 21.7 - - + +
34A GLY 4.0 6.7 - - - +
37A PHE* 3.4 31.0 - + + -
130A THR* 3.9 13.8 + - - -
131A ARG 2.7 37.9 + - - +
132A ASN* 3.3 41.2 - - + +
133A ILE* 2.9 27.2 + - - +
171A VAL* 3.8 10.5 - - + -
172A ASP* 1.3 74.3 - - - +
174A GLU* 1.3 84.2 + - - +
175A LEU* 4.0 6.7 - - + -
180A LEU* 3.1 41.5 - - + -
181A VAL 3.1 14.1 - - - +
182A CYS* 3.8 1.1 - - + +
183A VAL 4.3 1.3 - - - +
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Residues in contact with GLU 174 (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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132A ASN* 4.6 0.9 - - - -
133A ILE* 3.7 12.4 - - + +
134A SER* 3.6 20.0 + - - +
173A TRP* 1.3 90.4 - - - +
175A LEU* 1.3 60.5 + - - +
176A ASN* 3.3 27.3 + - - +
180A LEU* 3.5 1.0 - - - -
181A VAL* 2.7 45.7 + - + +
183A VAL* 3.7 22.7 - - + +
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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