Contacts of the strand formed by residues 191 - 203 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E HIS* 3.3 3.5 - - - +
147E SER* 2.7 43.2 + - - +
182E SER* 3.4 22.9 - - - +
183E VAL 3.4 11.0 - - - +
184E THR* 4.2 10.5 - - - +
190E GLU* 1.3 78.6 + - - +
192E TYR* 1.3 56.0 + - - +
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Residues in contact with TYR 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 5.8 1.4 + - - -
89E TYR* 4.7 8.7 - - - +
142E SER 4.4 9.9 - - - +
143E TRP 4.4 7.4 - - - -
144E THR* 3.6 20.7 + - - -
145E HIS 3.4 20.2 - - - +
146E HIS* 3.4 31.4 - - + +
147E SER 4.4 2.0 - - - +
181E ASN 4.0 0.2 - - - +
182E SER* 4.5 0.4 - - - -
183E VAL* 2.9 32.1 + - - +
185E TYR* 4.0 28.3 + + + -
187E CYS* 5.7 0.2 - - - -
188E CYS* 3.7 33.6 - - + +
190E GLU* 3.3 27.0 - - + +
191E ALA* 1.3 75.1 - - - +
193E GLU* 1.3 64.9 + - - +
194E ASP* 4.0 2.4 + - - +
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Residues in contact with GLU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TYR* 5.2 1.4 + - - -
141E GLY* 3.5 16.5 - - - -
142E SER* 3.8 7.4 + - - +
145E HIS 5.3 1.4 + - - -
147E SER* 4.0 26.2 - - - +
150E ILE 4.4 8.4 + - - +
151E SER* 3.1 17.9 - - - -
152E VAL* 3.0 31.1 + - + +
180E LYS* 2.4 34.0 + - - +
181E ASN 3.2 11.2 - - - +
182E SER* 4.3 10.1 + - - +
192E TYR* 1.3 78.2 - - - +
194E ASP* 1.3 62.8 + - - +
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Residues in contact with ASP 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TYR* 4.9 2.5 - - + -
139E LYS* 3.4 37.8 - - + -
140E ILE 3.1 15.7 - - - +
141E GLY* 4.2 1.8 - - - -
152E VAL* 3.6 9.8 - - - +
180E LYS* 3.5 3.3 - - - +
181E ASN* 2.8 59.9 + - - +
183E VAL* 3.5 22.2 - - - +
185E TYR* 4.3 1.8 + - - +
192E TYR 4.4 0.9 - - - +
193E GLU* 1.3 76.6 - - - +
195E VAL* 1.3 61.1 + - - +
196E GLU* 3.8 10.8 - - - +
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 4.9 16.2 - - + +
138E ILE 3.5 2.8 - - - +
139E LYS* 3.5 0.9 - - - -
140E ILE* 2.7 40.4 + - + +
152E VAL* 3.9 15.9 - - + +
153E ASP* 4.0 29.2 - - - +
154E PRO* 4.0 19.3 - - + -
178E GLN* 4.3 9.4 - - + +
179E LYS 3.5 7.2 - - - +
180E LYS* 4.7 1.6 - - + -
194E ASP* 1.3 81.4 - - - +
196E GLU* 1.3 65.3 + - - +
197E VAL* 4.1 20.9 - - + +
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Residues in contact with GLU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ARG* 3.3 37.8 + - + -
138E ILE 3.4 1.8 - - - -
139E LYS* 4.1 24.1 - - + +
177E THR 3.7 1.2 - - - +
178E GLN* 3.4 2.1 - - - -
179E LYS* 2.6 56.5 + - + +
181E ASN* 3.4 22.3 + - - +
194E ASP* 3.8 8.7 + - - +
195E VAL* 1.3 74.5 - - - +
197E VAL* 1.3 63.9 + - - +
198E SER* 3.7 2.6 + - - +
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Residues in contact with VAL 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 6.5 1.3 - - + -
32E SER* 5.9 0.9 - - - -
33E LEU* 3.9 27.6 - - + +
35E PHE* 4.0 20.6 - - + -
136E CYS 3.4 3.3 - - - +
137E ARG* 3.4 2.4 - - - -
138E ILE* 2.9 42.5 + - + +
140E ILE* 5.3 4.3 - - + -
176E VAL* 3.7 19.3 - - + -
177E THR 3.5 3.1 - - - +
178E GLN* 3.7 29.6 - - - +
195E VAL* 4.1 16.2 - - + +
196E GLU* 1.3 72.8 - - - +
198E SER* 1.3 61.0 + - - +
199E LEU* 3.6 0.9 + - - +
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Residues in contact with SER 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E THR* 3.9 18.8 - - - +
136E CYS 3.7 3.6 - - - -
137E ARG* 3.8 20.6 - - - +
175E ASP 3.7 0.3 - - - +
176E VAL* 3.3 9.5 - - - +
177E THR* 2.7 49.4 + - - -
196E GLU* 3.7 3.6 + - - +
197E VAL* 1.3 70.5 - - - +
199E LEU* 1.3 61.4 + - - +
200E ASN* 3.7 1.8 + - - +
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Residues in contact with LEU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PHE* 3.8 51.1 - - + -
38E ILE* 3.9 24.2 - - + -
48E VAL* 6.4 0.4 - - + -
50E VAL* 4.8 8.5 - - + -
134E ALA 3.6 1.6 - - - +
135E THR* 3.3 2.5 - - - -
136E CYS* 2.7 50.5 + - + +
138E ILE* 5.6 2.9 - - + -
173E ILE* 4.0 23.3 - - + -
175E ASP 4.0 0.9 - - - -
176E VAL* 4.0 12.8 - - + -
197E VAL 3.6 1.4 + - - +
198E SER* 1.3 72.0 - - - +
200E ASN* 1.3 60.9 + - - +
201E PHE* 3.7 16.7 - - + -
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Residues in contact with ASN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E SER 3.3 22.0 + - - +
133E GLY 3.9 1.6 + - - -
134E ALA 2.7 26.4 + - - -
135E THR* 3.1 20.0 + - + +
173E ILE* 3.6 2.4 - - - +
174E LEU* 2.7 53.0 + - - +
175E ASP* 2.8 32.2 + - + +
198E SER 3.7 1.3 + - - +
199E LEU* 1.3 71.3 - - - +
201E PHE* 1.3 56.4 + - - +
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Residues in contact with PHE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE* 3.6 31.4 - - + -
41E VAL* 3.6 24.9 - - + -
48E VAL* 4.1 21.3 - - + -
124E ASP 5.3 0.2 - - - -
125E VAL* 4.8 3.8 - - + -
128E VAL* 3.8 18.3 - - + +
133E GLY* 3.3 3.5 - - - -
134E ALA* 2.9 48.5 + - + +
136E CYS* 4.0 22.2 - - + -
171E PHE* 4.0 12.1 - + + -
172E GLU 3.2 15.7 - - - +
173E ILE* 4.4 2.7 - - + -
174E LEU* 4.2 3.6 - - - +
199E LEU* 3.7 22.2 - - + -
200E ASN* 1.3 74.8 - - - +
202E ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E VAL* 3.2 17.5 - - - +
130E THR 3.6 14.6 - - - +
131E GLU* 2.9 47.6 + - - +
133E GLY* 3.8 3.1 - - - -
171E PHE* 3.2 9.6 - - - -
172E GLU* 2.6 61.0 + - + +
174E LEU* 3.5 24.3 - - + +
201E PHE* 1.3 78.3 - - - +
203E LYS* 1.3 72.2 + - - +
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Residues in contact with LYS 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E VAL* 3.0 11.0 + - + +
129E ASP* 3.8 39.8 + - + +
130E THR 5.4 0.2 - - - +
170E ARG* 3.8 32.4 - - + +
171E PHE* 3.7 25.7 - - + -
202E ARG* 1.3 89.0 + - - +
204E LYS* 1.3 69.9 + - - +
205E GLY 3.9 0.9 + - - -
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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