Contacts of the strand formed by residues 168 - 176 (chain A) in PDB entry 1XU2
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 THR 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A THR* 2.8 5.1 + - - +
167A PHE* 1.3 111.7 - - + +
169A MET* 1.3 69.6 + - - +
188A ILE* 4.5 2.9 - - + -
189A ARG 3.4 8.1 - - - +
190A SER* 4.0 15.7 - - - +
222A ARG* 2.9 44.3 + - - -
197B ARG 4.1 1.1 - - - +
199B TYR* 4.0 22.7 - - + +
17R LEU* 4.6 2.5 - - - -
18R LEU* 3.6 13.3 - - + +
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Residues in contact with MET 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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162A PHE* 3.6 42.8 - - + -
164A ASP* 3.6 30.1 - - + +
166A THR* 3.7 18.6 - - - +
168A THR* 1.3 82.5 - - - +
170A GLY* 1.3 58.7 + - - +
188A ILE* 3.6 2.8 - - - -
189A ARG* 2.8 32.5 + - - +
191A MET* 3.9 22.4 - - + -
220A ILE* 3.8 8.1 - - + -
222A ARG* 3.6 17.3 - - + +
225A ALA* 3.7 21.3 - - + -
17R LEU* 3.6 9.4 - - - +
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Residues in contact with GLY 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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162A PHE* 3.4 15.4 - - - -
169A MET* 1.3 79.7 - - - +
171A GLN* 1.3 67.4 + - - +
187A CYS 3.1 13.7 - - - -
202A CYS* 4.4 1.8 - - - -
220A ILE* 3.5 27.1 - - - +
221A PRO* 3.8 3.5 - - - +
222A ARG* 5.1 0.2 - - - +
17R LEU* 3.7 9.1 - - - +
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Residues in contact with GLN 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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158A SER* 3.1 37.7 + - - +
160A VAL* 3.5 26.2 - - + +
170A GLY* 1.3 79.2 - - - +
172A VAL* 1.3 64.1 + - - +
173A VAL* 4.6 6.1 - - + -
185A PHE* 4.1 1.8 - - + +
186A ARG* 3.2 6.9 - - - +
187A CYS* 3.0 42.6 + - + +
202A CYS* 3.0 39.4 + - - +
204A SER* 4.6 1.2 - - - +
218A VAL* 4.2 13.5 - - + -
219A LYS 3.3 10.1 - - - +
220A ILE* 4.4 4.7 - - + -
17R LEU* 4.2 0.8 - - - +
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Residues in contact with VAL 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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171A GLN* 1.3 77.2 - - - +
173A VAL* 1.3 62.8 + - - +
174A SER* 3.7 13.6 + - - +
183A THR* 3.7 29.4 - - + +
185A PHE 3.7 3.1 - - - -
186A ARG* 4.0 14.6 - - + -
217A THR* 3.5 2.1 + - - +
218A VAL* 3.5 2.6 - - - -
219A LYS* 2.8 37.5 + - + +
221A PRO* 3.6 27.6 - - + -
16R SER 4.2 10.8 - - - +
17R LEU* 4.1 7.0 - - + -
19R HIS* 5.8 2.2 - - + -
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Residues in contact with VAL 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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156A LEU* 3.8 28.0 - - + -
158A SER* 4.1 16.6 - - - +
171A GLN* 4.6 4.9 - - + -
172A VAL* 1.3 73.1 - - - +
174A SER* 1.3 64.9 + - - +
183A THR* 3.8 1.2 - - - +
184A LEU* 2.8 27.3 + - + +
185A PHE* 2.9 51.9 + - + +
216A ILE* 4.0 9.2 - - + -
217A THR 3.3 9.0 - - - +
218A VAL* 4.1 16.2 - - + -
236A LEU* 5.4 2.5 - - + -
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Residues in contact with SER 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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172A VAL* 3.7 18.7 + - - +
173A VAL* 1.3 77.0 + - - +
175A ARG* 1.3 61.1 + - - +
176A GLU* 5.3 0.7 - - - -
181A ARG* 4.5 18.9 + - - -
182A GLU 3.3 16.4 - - - -
183A THR* 4.0 6.9 + - - -
184A LEU* 4.2 5.6 - - - +
215A ILE 4.3 0.2 - - - -
216A ILE* 3.2 11.6 - - - +
217A THR* 3.0 41.9 + - - -
219A LYS* 6.1 0.5 - - - +
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Residues in contact with ARG 175 (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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174A SER* 1.3 75.5 - - - +
176A GLU* 1.3 63.8 + - - +
177A GLY 5.2 3.0 + - - +
178A GLN* 5.0 4.9 + - - -
180A ARG* 3.7 8.2 + - - +
181A ARG* 3.7 1.0 - - - -
182A GLU* 3.0 58.5 + - + +
184A LEU* 3.9 22.8 - - + +
209A HIS* 3.3 20.8 + - - +
210A LEU* 4.5 3.9 - - + +
211A HIS* 3.0 37.0 + - - -
214A ASP* 3.2 25.0 + - - +
215A ILE 3.2 5.4 - - - +
216A ILE* 3.5 21.8 - - + -
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Residues in contact with GLU 176 (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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174A SER* 5.3 0.2 - - - -
175A ARG* 1.3 78.8 - - - +
177A GLY* 1.3 58.6 + - - +
180A ARG 3.4 7.6 - - - +
181A ARG* 4.0 24.9 - - + +
213A GLY 4.3 0.7 - - - +
214A ASP* 3.3 7.7 - - - +
215A ILE* 2.9 50.6 + - + +
217A THR* 3.7 26.9 + - + +
219A LYS* 4.3 11.8 + - - -
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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