Contacts of the strand formed by residues 141 - 150 (chain E) in PDB entry 5MWF
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 SER 141 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E TYR* 3.3 31.2 + - - +
90E TYR* 4.1 8.8 + - - -
139E PRO* 2.6 30.5 + - - +
140E ARG* 1.3 76.7 - - - +
142E PHE* 1.3 62.8 + - - +
170E GLY 3.6 6.5 - - - -
171E MET* 4.2 17.9 - - - +
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Residues in contact with PHE 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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30E PHE* 4.2 6.7 - + - -
75E LEU* 3.8 17.3 - - + -
76E LYS 3.6 12.3 - - - +
78E TYR* 3.3 21.2 - - - +
90E TYR* 4.3 6.3 - - + -
138E TRP* 4.3 16.2 - + + -
140E ARG 3.4 11.2 - - - -
141E SER* 1.3 75.7 - - - +
143E THR* 1.3 81.1 + - - +
144E LEU* 4.0 20.9 - - + -
168E HIS* 4.6 11.2 - + - -
169E ALA* 3.5 0.2 - - - -
170E GLY* 3.1 51.4 + - - -
171E MET 3.6 6.5 - - - -
172E ILE* 3.6 24.0 - - + -
194E ILE* 3.8 28.7 - - + -
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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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74E CYS 3.9 0.5 - - - +
75E LEU* 3.7 4.7 - - - +
76E LYS* 3.0 48.7 + - - +
77E GLU 3.1 12.9 + - - -
79E GLN* 3.1 26.7 + - - +
82E VAL* 4.0 26.7 - - + -
142E PHE* 1.3 85.8 + - - +
144E LEU* 1.3 65.5 + - - +
145E ILE* 4.2 3.3 + - + +
168E HIS 3.5 10.1 - - - +
169E ALA* 3.4 5.9 - - - +
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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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30E PHE* 4.4 6.1 - - + -
32E LEU* 3.8 23.8 - - + -
73E VAL* 3.7 24.0 - - + -
74E CYS 3.6 11.4 - - - +
75E LEU* 4.2 9.9 - - + -
142E PHE* 4.0 15.4 - - + -
143E THR* 1.3 74.1 - - - +
145E ILE* 1.3 67.2 + - - +
146E VAL* 3.9 15.4 - - + +
167E SER* 3.2 3.3 - - - -
168E HIS* 2.6 44.9 + - + +
181E LEU* 4.3 16.6 - - + -
183E PHE* 4.9 5.4 - - + -
192E LEU* 4.6 2.9 - - + -
194E ILE* 3.9 18.2 - - + -
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Residues in contact with ILE 145 (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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72E ARG 3.9 0.7 - - - +
73E VAL* 3.7 2.4 - - - -
74E CYS* 2.9 54.7 + - + +
76E LYS* 4.0 19.7 - - + +
82E VAL* 4.3 5.6 - - + -
83E THR 3.5 24.7 - - - +
84E PRO* 4.3 12.1 - - + +
85E THR 6.0 0.2 - - - -
143E THR* 4.5 7.0 - - + +
144E LEU* 1.3 80.0 - - - +
146E VAL* 1.3 64.9 + - - +
147E GLU* 4.3 8.0 + - + +
165E ARG* 3.8 27.6 - - + +
166E VAL 3.3 8.3 - - - +
167E SER* 4.0 12.6 - - - -
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Residues in contact with VAL 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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32E LEU* 4.1 9.9 - - + -
34E LEU* 6.4 0.2 - - + -
71E VAL* 3.7 25.6 - - + -
72E ARG 3.6 3.1 - - - +
73E VAL* 4.9 3.4 - - + -
144E LEU* 3.9 26.0 - - + -
145E ILE* 1.3 77.0 - - - +
147E GLU* 1.3 64.2 + - - +
164E GLU 4.1 0.3 - - - +
165E ARG* 3.4 1.7 - - - +
166E VAL* 2.8 50.5 + - + +
183E PHE* 5.1 3.6 - - + -
190E LEU* 3.9 22.2 - - + +
192E LEU* 4.1 20.6 - - + -
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Residues in contact with GLU 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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71E VAL* 3.2 13.4 - - - +
72E ARG* 2.9 50.7 + - - +
74E CYS* 6.2 3.1 - - + -
84E PRO 5.0 0.5 - - - +
145E ILE* 4.5 6.6 - - + +
146E VAL* 1.3 79.4 - - - +
148E ALA* 1.3 60.7 + - - +
149E TRP* 2.6 40.8 + - + +
162E LEU* 4.0 3.1 - - + -
164E GLU 3.3 5.2 - - - +
165E ARG* 2.6 52.6 + - + +
190E LEU* 5.7 1.3 - - - -
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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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37E LEU* 4.3 20.2 - - + -
69E THR* 4.1 16.6 - - + -
70E TYR 3.7 4.0 - - - -
71E VAL* 4.7 3.1 - - + +
147E GLU* 1.3 74.0 - - - +
149E TRP* 1.3 57.8 + - - +
162E LEU* 3.3 3.8 - - - +
163E ILE* 2.8 47.0 + - + +
164E GLU* 2.8 21.9 + - + +
190E LEU* 5.4 3.1 - - + -
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Residues in contact with TRP 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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69E THR* 3.5 4.2 - - - +
70E TYR* 2.7 69.1 + - + +
72E ARG* 3.3 36.0 - - + +
147E GLU* 2.6 47.3 + - + -
148E ALA* 1.3 69.9 - - - +
150E ASP* 1.3 59.7 + - - +
158E ASN 3.1 28.3 - - - -
159E GLU* 4.8 5.4 - - - -
161E LEU* 3.0 35.2 - - + -
162E LEU* 3.4 23.4 - - + +
163E ILE* 3.4 4.9 - - - -
165E ARG* 5.1 2.5 - - - -
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Residues in contact with ASP 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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44E LEU* 4.3 6.9 - - + +
50E CYS* 3.6 12.1 - - - +
67E CYS* 3.2 23.6 - - + -
68E ASP 3.4 2.6 + - - -
70E TYR* 3.8 8.9 + - - -
149E TRP* 1.3 74.4 - - - +
151E TRP* 1.3 70.6 + - - +
152E ASP* 3.4 5.4 + - - +
161E LEU* 3.0 41.7 + - + +
163E ILE* 3.1 20.3 - - + +
405E CA 2.4 25.7 - - - -
406E CA 2.8 24.8 - - - -
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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