Contacts of the strand formed by residues 171 - 184 (chain A) in PDB entry 3U8M
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.5 39.5 - - + -
39A LEU 4.8 2.0 - - - -
41A VAL* 3.5 34.1 - - + -
128A VAL* 4.0 2.7 - - + -
165A PHE* 3.4 16.6 - - - -
166A SER 4.8 0.3 - - - +
169A SER* 3.0 9.6 + - - +
170A ARG* 1.3 115.9 - - + +
172A GLU* 1.3 62.3 + - - +
201A PHE* 4.0 18.6 - + + -
202A ARG 3.4 10.5 - - - +
203A LYS* 3.4 51.4 - - + -
204A LYS* 3.5 15.8 + - - +
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Residues in contact with GLU 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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165A PHE* 4.1 6.3 - - - -
171A PHE* 1.3 77.9 - - - +
173A ILE* 1.3 65.9 + - - +
174A LEU* 3.8 7.2 + - + +
201A PHE* 3.3 6.2 - - - +
202A ARG* 2.8 74.5 + - + +
203A LYS 4.5 2.9 - - - +
204A LYS* 4.1 25.6 - - + +
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Residues in contact with ILE 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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35A PHE* 3.7 22.7 - - + -
38A ILE* 4.9 4.3 - - + -
161A ASP* 4.2 14.7 - - + +
162A SER* 3.4 24.5 + - - +
165A PHE* 3.4 46.2 - - + -
172A GLU* 1.3 75.9 - - - +
174A LEU* 1.3 67.4 + - - +
175A ASP 3.7 22.2 - - - +
176A VAL* 3.8 13.0 - - + -
199A LEU* 4.1 15.3 - - + -
200A ASN 3.9 4.0 - - - +
201A PHE* 4.5 0.7 - - + -
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Residues in contact with LEU 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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131A GLU 3.9 8.1 - - - +
132A SER 3.8 17.0 - - - +
133A GLY* 4.2 3.1 - - - -
161A ASP* 4.2 4.1 - - - +
172A GLU* 4.5 7.6 - - + -
173A ILE* 1.3 81.1 - - - +
175A ASP* 1.3 62.6 + - + +
200A ASN* 2.7 37.0 + - - +
201A PHE* 4.4 4.9 - - - -
202A ARG* 3.5 54.7 - - + +
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Residues in contact with ASP 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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161A ASP* 3.3 14.8 - - - +
173A ILE* 3.6 2.1 - - - +
174A LEU* 1.3 83.1 - - - +
176A VAL* 1.3 76.5 + - - +
177A THR* 3.6 22.2 - - + +
198A SER 4.4 0.4 - - - -
200A ASN* 2.9 41.3 + - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU 5.1 3.8 - - - +
35A PHE* 4.1 15.5 - - + -
161A ASP* 3.5 28.4 + - + +
173A ILE* 3.8 17.9 - - + -
175A ASP* 1.3 86.7 + - - +
177A THR* 1.3 68.2 + - - +
178A GLN* 4.5 11.6 - - + +
197A VAL* 3.8 28.9 - - + -
198A SER 3.4 5.8 - - - +
199A LEU* 4.0 13.2 - - + -
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Residues in contact with THR 177 (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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175A ASP* 3.6 21.3 - - - +
176A VAL* 1.3 78.3 - - - +
178A GLN* 1.3 65.4 + - - +
196A GLU 3.8 0.5 - - - +
197A VAL* 3.5 3.1 - - - +
198A SER* 2.7 53.9 + - - -
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Residues in contact with GLN 178 (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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31A VAL 3.4 14.4 - - - +
32A SER* 4.0 8.6 + - - +
33A LEU 3.7 27.9 + - - +
154A PRO* 3.3 37.1 - - + +
155A THR 4.1 3.1 + - - -
176A VAL* 4.5 8.4 - - + +
177A THR* 1.3 81.2 - - - +
179A LYS* 1.3 60.9 + - - +
195A VAL* 4.5 5.2 - - + +
196A GLU 3.5 4.7 - - - +
197A VAL* 3.8 23.8 - - + +
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Residues in contact with LYS 179 (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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154A PRO* 4.9 1.1 - - - -
177A THR 4.3 0.2 - - - -
178A GLN* 1.3 76.3 - - - +
180A LYS* 1.3 69.2 + - - +
181A ASN* 3.3 24.6 + - - +
195A VAL* 3.4 4.6 - - - -
196A GLU* 2.6 59.4 + - + +
198A SER* 6.2 0.4 - - - +
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Residues in contact with LYS 180 (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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151A SER* 4.9 0.8 - - - -
152A VAL 2.8 21.1 + - - +
153A ASP* 3.4 28.3 + - - +
154A PRO* 4.2 17.6 - - + +
179A LYS* 1.3 80.9 - - - +
181A ASN* 1.3 76.8 + - - +
182A SER* 6.4 1.1 - - - -
193A GLU* 2.7 38.1 + - - +
194A ASP 3.6 7.4 - - - +
195A VAL* 4.5 2.2 - - + +
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Residues in contact with ASN 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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179A LYS* 3.3 34.9 + - - +
180A LYS* 1.3 82.4 - - - +
182A SER* 1.3 61.3 + - - +
183A VAL* 4.2 8.5 - - + -
193A GLU* 3.4 7.4 - - - +
194A ASP* 2.9 60.2 + - - +
196A GLU* 3.3 31.6 + - - +
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Residues in contact with SER 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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147A SER* 4.6 3.5 - - - -
180A LYS* 6.4 0.9 - - - -
181A ASN* 1.3 75.9 - - - +
183A VAL* 1.3 62.5 + - - +
184A THR* 4.4 0.3 + - - -
191A ALA* 3.7 20.1 - - - +
192A TYR 3.8 3.8 - - - -
193A GLU* 4.1 18.4 + - - +
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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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139A LYS* 4.8 4.7 - - - +
181A ASN* 4.3 8.5 - - + -
182A SER* 1.3 80.1 + - - +
184A THR* 1.3 70.7 + - - +
185A TYR* 3.4 41.3 - - + +
191A ALA* 4.2 1.6 - - - -
192A TYR 2.7 38.1 + - - +
194A ASP* 3.3 23.8 - - - +
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Residues in contact with THR 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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182A SER 4.4 0.2 + - - -
183A VAL* 1.3 81.8 - - - +
185A TYR* 1.3 65.2 + - - +
186A SER 4.3 0.2 + - - -
188A CYS 3.9 8.1 - - - +
189A PRO* 3.9 14.1 - - + +
190A GLU 3.8 14.6 - - - +
191A ALA* 4.0 12.6 - - - +
163B GLU* 5.5 1.2 - - - +
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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