Contacts of the strand formed by residues 191 - 203 (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 ALA 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A HIS* 3.0 5.7 - - - +
147A SER* 2.7 41.7 + - - +
182A SER* 3.7 20.4 - - - +
183A VAL 3.4 9.4 - - - +
184A THR* 4.0 13.0 - - - +
190A GLU* 1.3 78.8 + - - +
192A TYR* 1.3 55.7 + - - +
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Residues in contact with TYR 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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89A TYR* 4.7 8.3 - - - +
142A SER 4.6 4.7 - - - +
143A TRP 4.4 9.4 - - - -
144A THR* 3.4 31.9 + - - -
145A HIS 3.5 9.9 - - - +
146A HIS* 3.5 31.9 - - + +
182A SER* 4.5 0.2 - - - -
183A VAL* 2.7 37.1 + - - +
185A TYR* 3.8 30.6 + + + -
187A CYS* 5.4 1.6 - - - -
188A CYS* 3.7 33.7 - - + +
190A GLU* 3.4 24.4 - - + +
191A ALA* 1.3 75.9 - - - +
193A GLU* 1.3 65.8 + - - +
194A ASP* 4.0 1.2 + - - +
104B ARG* 5.7 2.9 + - - +
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Residues in contact with GLU 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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89A TYR* 5.0 1.8 + - - -
141A GLY* 3.6 14.0 - - - -
142A SER* 3.8 10.4 + - - +
145A HIS 5.1 2.6 + - - -
147A SER* 3.7 32.6 - - - +
150A ILE* 4.3 5.3 + - + +
151A SER* 3.1 18.3 - - - -
152A VAL* 3.0 31.2 + - + +
180A LYS* 2.7 32.9 + - - +
181A ASN 3.4 9.4 - - - +
182A SER* 4.1 12.9 + - - +
185A TYR* 6.0 0.2 - - - -
192A TYR* 1.3 76.4 - - - +
194A ASP* 1.3 62.0 + - - +
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Residues in contact with ASP 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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89A TYR* 4.7 3.4 - - + -
139A LYS* 3.3 32.1 - - + -
140A ILE 3.3 14.8 - - - +
141A GLY* 4.2 2.2 - - - +
152A VAL* 3.6 8.9 - - - +
180A LYS* 3.6 2.1 - - - +
181A ASN* 2.9 56.4 + - - +
183A VAL* 3.3 30.3 - - - +
185A TYR* 3.9 2.8 + - - +
193A GLU* 1.3 76.5 - - - +
195A VAL* 1.3 61.0 + - - +
196A GLU* 3.9 9.9 - - - +
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Residues in contact with VAL 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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31A VAL* 4.7 17.3 - - + +
138A ILE 3.6 2.1 - - - +
139A LYS* 3.6 1.6 - - - -
140A ILE* 2.7 41.0 + - + +
152A VAL* 4.0 23.1 - - + +
153A ASP 4.1 22.0 - - - +
154A PRO* 4.1 17.7 - - + -
178A GLN* 4.5 9.9 - - + +
179A LYS 3.4 8.3 - - - +
180A LYS* 4.7 1.8 - - + -
194A ASP* 1.3 79.9 - - - +
196A GLU* 1.3 63.4 + - - +
197A VAL* 3.9 20.3 + - + +
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Residues in contact with GLU 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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137A ARG* 3.8 37.9 + - + +
138A ILE 3.5 2.7 - - - +
139A LYS* 4.1 25.6 - - + +
177A THR 3.8 0.2 - - - +
178A GLN* 3.5 1.6 - - - -
179A LYS* 2.6 57.1 + - + +
181A ASN* 3.3 25.1 + - - +
194A ASP* 3.9 8.8 + - - +
195A VAL* 1.3 71.7 - - - +
197A VAL* 1.3 62.0 + - - +
198A SER* 3.7 4.5 + - - +
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Residues in contact with VAL 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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31A VAL* 6.0 1.8 - - + +
32A SER* 5.9 0.7 - - - -
33A LEU* 4.0 29.8 - - + +
35A PHE* 4.0 20.2 - - + -
136A CYS 3.3 2.6 - - - +
137A ARG* 4.6 0.4 - - - -
138A ILE* 2.8 44.3 + - + +
140A ILE* 5.3 4.7 - - + -
176A VAL* 3.8 25.8 - - + -
177A THR 3.5 3.4 - - - +
178A GLN* 3.8 20.6 - - - +
195A VAL* 4.1 16.8 - - + +
196A GLU* 1.3 74.8 - - - +
198A SER* 1.3 63.1 + - - +
199A LEU* 3.6 0.5 + - - +
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Residues in contact with SER 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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135A THR* 4.1 18.4 - - - +
136A CYS 3.6 4.7 - - - -
137A ARG* 4.2 16.0 - - - +
175A ASP 3.8 0.2 - - - +
176A VAL* 3.4 6.9 - - - -
177A THR* 2.7 48.9 + - - +
179A LYS* 6.2 0.3 - - - +
196A GLU* 3.7 4.9 + - - +
197A VAL* 1.3 72.2 - - - +
199A LEU* 1.3 61.9 + - - +
200A ASN* 3.7 2.0 + - - +
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Residues in contact with LEU 199 (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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35A PHE* 3.8 52.5 - - + -
38A ILE* 4.0 23.6 - - + -
48A VAL* 6.4 0.2 - - + -
50A VAL* 4.8 9.4 - - + -
134A ALA 3.4 2.1 - - - +
135A THR* 3.3 2.2 - - - -
136A CYS* 2.7 50.5 + - + +
138A ILE* 5.5 2.2 - - + -
173A ILE* 4.1 22.0 - - + -
175A ASP 4.0 0.4 - - - -
176A VAL* 4.0 12.6 - - + +
197A VAL 3.6 1.6 + - - +
198A SER* 1.3 72.2 - - - +
200A ASN* 1.3 60.3 + - - +
201A PHE* 3.7 17.0 - - + -
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Residues in contact with ASN 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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132A SER 3.2 23.4 + - - +
133A GLY* 3.8 1.6 - - - -
134A ALA 2.7 24.2 + - - -
135A THR* 3.2 20.3 + - + +
173A ILE* 3.7 1.7 - - - +
174A LEU* 2.7 53.0 + - - +
175A ASP* 2.9 32.4 + - + +
198A SER* 3.7 1.9 + - - +
199A LEU* 1.3 71.8 - - - +
201A PHE* 1.3 54.6 + - - +
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Residues in contact with PHE 201 (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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38A ILE* 3.5 32.3 - - + -
41A VAL* 3.7 17.7 - - + -
48A VAL* 4.1 22.0 - - + -
124A ASP 5.2 0.7 - - - -
125A VAL* 4.7 3.8 - - + -
128A VAL* 3.7 22.8 - - + +
133A GLY* 3.1 3.4 - - - -
134A ALA* 2.6 61.3 + - + +
136A CYS* 4.0 20.9 - - + -
171A PHE* 4.0 11.4 - + + -
172A GLU 3.3 16.8 - - - +
173A ILE* 4.5 2.5 - - - -
174A LEU* 4.3 2.9 - - - +
199A LEU* 3.7 20.0 - - + -
200A ASN* 1.3 75.5 - - - +
202A ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 202 (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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128A VAL* 3.0 15.3 - - - +
130A THR 3.5 22.7 - - - +
131A GLU* 3.0 39.5 + - - +
133A GLY* 3.6 4.0 - - - -
171A PHE* 3.4 8.7 - - - +
172A GLU* 2.8 55.8 + - + +
174A LEU* 3.5 27.7 - - + +
201A PHE* 1.3 79.3 - - - +
203A LYS* 1.3 74.4 + - - +
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Residues in contact with LYS 203 (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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41A VAL* 4.9 10.8 + - - -
128A VAL* 2.8 32.5 + - + +
129A ASP* 3.8 36.7 + - - +
130A THR 5.4 0.2 - - - +
170A ARG* 3.9 21.1 - - + +
171A PHE* 3.4 34.8 - - + -
202A ARG* 1.3 89.8 + - - +
204A LYS* 1.3 66.9 + - - +
205A GLY 3.9 0.7 + - - -
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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