Contacts of the strand formed by residues 141 - 151 (chain E) in PDB entry 4NQC
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 LYS 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136D ASP* 5.8 0.6 + - - -
161D MET* 4.0 14.8 - - + -
164D MET* 5.9 3.6 - - - -
166D PHE* 3.7 54.6 - - + -
135E GLU* 3.6 5.7 - - - -
136E ILE* 3.4 23.9 + - - -
139E THR* 3.1 33.2 + - - +
140E GLN* 1.4 81.0 - - - +
142E ALA* 1.3 60.0 + - - +
196E ARG* 3.7 18.6 - - + +
197E VAL 3.5 11.7 - - - +
198E SER* 5.0 2.0 - - - -
199E ALA 3.9 3.1 - - - +
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Residues in contact with ALA 142 (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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131E PRO* 3.5 26.2 - - + -
135E GLU* 3.8 2.9 - - - -
136E ILE* 4.0 8.5 - - + -
141E LYS* 1.3 74.3 - - - +
143E THR* 1.4 61.0 + - - +
144E LEU* 4.0 0.7 + - - +
195E LEU 3.7 1.4 - - - +
196E ARG* 3.5 2.0 - - - -
197E VAL* 2.7 44.0 + - + +
198E SER 4.4 2.2 - - - +
199E ALA* 4.6 2.0 - - - -
202E TRP* 3.7 24.7 - - + -
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Residues in contact with THR 143 (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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121D LEU* 3.4 11.8 - - - +
133D LEU* 3.8 30.6 - - + +
135D THR* 5.1 0.9 + - - -
159D LEU* 5.1 2.7 - - + -
170D SER* 5.9 0.4 - - - +
131E PRO* 3.4 21.6 - - - +
135E GLU* 2.6 35.8 + - - +
142E ALA* 1.4 70.5 - - - +
144E LEU* 1.3 70.5 + - - +
145E VAL* 4.2 1.1 - - + -
194E ARG* 4.0 20.4 - - + -
195E LEU 3.5 7.6 - - - +
196E ARG* 3.1 21.2 + - + +
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Residues in contact with LEU 144 (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* 4.1 18.8 - - + -
129E PHE 3.5 7.6 - - - +
130E GLU* 5.2 0.4 - - - -
131E PRO* 3.9 16.2 - - + -
142E ALA 4.4 0.2 - - - +
143E THR* 1.3 74.7 - - - +
145E VAL* 1.3 62.9 + - - +
160E TRP* 4.0 16.1 - - + -
193E SER 4.1 0.2 - - - +
194E ARG* 3.4 4.5 - - - -
195E LEU* 2.8 43.8 + - + +
197E VAL* 4.3 14.6 - - + -
202E TRP* 3.7 35.9 - - + -
209E PHE* 3.8 35.7 - - + -
240E ALA* 4.2 2.9 - - + -
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Residues in contact with VAL 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.8 23.6 - - + -
131D VAL* 4.0 15.3 - - + -
133D LEU* 4.0 26.5 - - + -
172D VAL* 4.1 11.7 - - + -
128E VAL* 3.4 3.8 - - - +
129E PHE* 2.7 41.4 + - + -
143E THR* 4.2 4.3 - - + -
144E LEU* 1.3 78.7 - - - +
146E CYS* 1.3 62.9 + - - +
147E LEU* 3.4 26.9 - - + -
160E TRP* 4.0 2.5 - - - -
192E SER* 4.9 0.7 - - - -
193E SER 3.4 10.1 - - - +
194E ARG* 4.4 4.7 - - + -
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Residues in contact with CYS 146 (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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126E VAL* 3.6 18.8 - - - -
127E ALA 3.4 6.7 - - - -
128E VAL* 4.1 0.9 - - + +
145E VAL* 1.3 72.6 - - - +
147E LEU* 1.3 68.0 + - - +
148E ALA 4.3 0.2 - - - -
158E LEU* 4.2 7.2 - - - -
160E TRP* 3.4 19.2 - - + -
191E LEU 3.9 0.4 - - - +
192E SER* 3.1 6.1 - - - -
193E SER* 2.8 36.0 + - - +
211E CYS* 2.0 50.3 - - + -
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Residues in contact with LEU 147 (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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131D VAL* 3.6 29.6 - - + -
172D VAL* 4.2 5.4 - - + -
174D TRP* 3.7 40.2 - - + +
125E GLU 3.2 5.2 - - - +
126E VAL* 3.4 1.3 - - - -
127E ALA* 3.0 31.6 + - + +
129E PHE* 4.0 19.5 - - + -
145E VAL* 3.4 23.6 - - + -
146E CYS* 1.3 86.1 - - - +
148E ALA* 1.3 59.1 + - - +
149E THR* 3.8 10.9 + - + -
191E LEU 3.4 3.1 - - - +
192E SER* 4.1 11.2 - - - -
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Residues in contact with ALA 148 (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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124E PRO* 4.1 12.3 - - + -
125E GLU 3.2 7.6 - - - -
126E VAL* 4.5 1.3 - - - -
146E CYS* 4.3 0.6 - - - -
147E LEU* 1.3 71.1 - - - +
149E THR* 1.3 59.6 + - - +
151E PHE* 3.5 14.2 - - + -
158E LEU* 4.5 3.6 - - + +
190E ALA* 3.2 2.8 - - - -
191E LEU* 2.7 48.5 + - + +
213E VAL* 3.9 31.0 - - + -
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Residues in contact with THR 149 (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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174D TRP* 4.1 16.6 - - + +
123E PRO 4.4 0.2 - - - +
124E PRO* 3.4 1.4 - - - +
125E GLU* 2.8 52.6 + - - +
147E LEU* 4.4 19.1 + - + -
148E ALA* 1.3 78.8 - - - +
150E GLY* 1.3 63.8 + - - +
151E PHE* 3.3 3.8 - - - -
180E GLU* 3.7 19.1 - - - +
189E TYR 3.5 3.8 - - - -
190E ALA* 3.9 10.1 - - + -
191E LEU 5.2 0.2 - - - +
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Residues in contact with GLY 150 (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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122E PHE* 3.3 22.9 - - - +
123E PRO 3.8 4.3 - - - +
125E GLU* 5.7 2.0 - - - -
149E THR* 1.3 72.0 - - - +
151E PHE* 1.3 59.7 + - - +
180E GLU* 3.0 20.5 + - - -
188E ARG* 3.4 20.4 + - - -
189E TYR 2.8 8.2 + - - -
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Residues in contact with PHE 151 (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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122E PHE 3.2 12.6 - - - +
123E PRO 4.0 0.2 - - - -
124E PRO* 3.6 32.8 - - + -
148E ALA* 3.5 29.2 - - + -
149E THR 3.3 0.2 - - - -
150E GLY* 1.3 78.4 - - - +
152E TYR* 1.3 60.1 + - - +
153E PRO 3.6 13.5 - - - -
154E ASP* 3.9 16.4 - - - -
156E VAL* 3.7 38.6 - - + -
177E PRO* 4.1 12.6 - - + -
188E ARG* 3.4 2.0 - - - -
189E TYR* 2.7 68.7 + - + -
190E ALA 4.0 0.9 - - - -
191E LEU* 4.0 10.3 - - + -
215E PHE* 4.5 2.2 - + + -
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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