Contacts of the helix formed by residues 137 - 151 (chain E) in PDB entry 4WFN
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 ASP 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E LEU* 3.9 11.3 - - + +
121E VAL* 6.5 0.2 - - + -
136E ILE* 1.3 87.1 - - + +
138E LYS* 1.3 59.6 + - - +
139E GLN* 2.9 26.9 + - - +
140E LEU* 3.2 38.4 - - + +
141E VAL* 3.0 30.7 + - - +
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Residues in contact with LYS 138 (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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70E THR* 6.3 0.2 - - - +
74E ASN* 3.6 40.9 + - + +
83E TYR* 3.5 32.9 - - + -
136E ILE 3.2 3.2 + - - -
137E ASP* 1.3 72.1 + - - +
139E GLN* 1.3 60.7 + - + +
141E VAL* 4.1 4.7 - - + +
142E GLY* 2.9 25.6 + - - -
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Residues in contact with GLN 139 (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 LEU* 5.2 16.0 - - + +
137E ASP* 2.9 11.7 + - - +
138E LYS* 1.3 79.4 - - + +
140E LEU* 1.3 69.5 + - + +
142E GLY* 3.4 1.9 + - - -
143E GLN* 2.9 31.2 + - - +
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Residues in contact with LEU 140 (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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118E PRO* 5.8 6.3 - - + -
121E VAL* 4.8 10.5 - - + -
136E ILE* 6.3 0.4 - - + -
137E ASP* 3.2 34.9 + - + +
139E GLN* 1.3 88.4 - - + +
141E VAL* 1.3 59.8 + - - +
142E GLY 3.2 0.2 - - - -
143E GLN* 3.9 6.9 - - + +
144E VAL* 2.9 36.1 + - + +
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E TYR* 4.2 14.6 - - + +
85E ILE* 3.8 28.9 - - + -
121E VAL* 4.5 12.5 - - + +
133E VAL* 4.1 15.1 - - + +
134E SER 4.4 2.5 - - - +
135E GLY* 3.8 35.7 - - - +
136E ILE 4.1 0.7 - - - +
137E ASP 3.0 22.4 + - - +
138E LYS* 4.1 6.1 - - + +
140E LEU* 1.3 74.5 - - - +
142E GLY* 1.3 66.8 + - - +
144E VAL* 3.3 5.9 + - - +
145E ALA* 2.9 24.6 + - - +
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Residues in contact with GLY 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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85E ILE* 4.8 8.1 - - - -
138E LYS 2.9 21.0 + - - -
139E GLN* 3.5 2.0 - - - -
141E VAL* 1.3 79.1 - - - +
143E GLN* 1.3 55.3 + - - +
145E ALA* 3.8 2.1 - - - +
146E ALA* 2.9 28.3 + - - +
149E ARG* 5.2 1.4 + - - -
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Residues in contact with GLN 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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139E GLN 2.9 17.0 + - - +
140E LEU* 4.0 9.2 - - + +
141E VAL 3.2 0.4 - - - -
142E GLY* 1.3 74.8 - - - +
144E VAL* 1.3 60.5 + - - +
146E ALA* 3.3 7.8 - - + +
147E ASN* 2.9 51.2 + - - +
150E LYS* 3.8 21.2 + - - +
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Residues in contact with VAL 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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115E ILE* 5.4 4.1 - - + +
117E PRO* 5.1 1.3 - - + -
118E PRO* 3.7 34.3 - - + -
121E VAL* 4.3 15.5 - - + -
123E PHE* 3.9 26.9 - - + -
133E VAL* 3.9 19.7 - - + -
140E LEU 2.9 21.4 + - - +
141E VAL 3.7 4.0 - - - +
143E GLN* 1.3 75.6 - - - +
145E ALA* 1.3 60.7 + - - +
147E ASN* 2.9 28.2 + - - +
148E VAL* 3.0 14.0 + - - +
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Residues in contact with ALA 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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85E ILE* 3.6 29.2 - - + -
87E LEU* 3.7 14.3 - - + +
133E VAL* 4.3 12.3 - - + -
141E VAL 2.9 16.9 + - - +
142E GLY 4.0 2.2 - - - +
144E VAL* 1.3 79.3 - - - +
146E ALA* 1.3 57.6 + - - +
148E VAL* 3.3 12.4 + - - +
149E ARG* 2.9 29.9 + - - +
164E PHE* 5.6 2.2 - - + -
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Residues in contact with ALA 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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142E GLY 2.9 21.5 + - - +
143E GLN* 3.3 16.6 - - + +
144E VAL 3.0 0.4 - - - -
145E ALA* 1.3 78.3 - - - +
147E ASN* 1.3 56.5 + - - +
149E ARG* 3.5 26.9 + - - +
150E LYS* 2.9 47.5 + - - +
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Residues in contact with ASN 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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115E ILE* 5.1 8.7 - - + +
143E GLN* 2.9 35.4 + - - +
144E VAL* 2.9 12.3 + - - +
146E ALA* 1.3 75.8 - - - +
148E VAL* 1.3 63.8 + - + +
150E LYS* 3.1 21.4 + - - +
151E VAL* 3.0 25.6 + - - +
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Residues in contact with VAL 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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87E LEU* 3.6 19.1 - - + -
103E LEU* 4.5 2.7 - - + -
105E MET* 4.2 11.9 - - - -
115E ILE* 3.5 20.6 - - + +
123E PHE* 3.9 20.4 - - + -
131E ILE* 3.8 24.7 - - + -
133E VAL* 4.8 1.8 - - + -
144E VAL 3.0 15.5 + - - +
145E ALA* 3.5 11.9 - - - +
147E ASN* 1.3 76.3 - - - +
149E ARG* 1.3 61.1 + - - +
151E VAL* 3.2 25.0 - - - +
162E VAL* 3.2 14.6 - - + +
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Residues in contact with ARG 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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87E LEU* 4.6 7.4 - - + -
142E GLY 5.2 1.0 + - - -
145E ALA 2.9 15.6 + - - +
146E ALA* 3.6 27.7 + - - +
148E VAL* 1.3 75.2 - - - +
150E LYS* 1.3 63.7 + - + +
151E VAL 3.0 1.2 + - - -
152E ARG 2.9 25.6 + - - +
153E LYS* 4.1 3.0 + - - +
154E PRO* 6.1 1.1 - - + -
162E VAL* 3.7 29.5 - - + +
163E ARG* 5.5 0.4 - - - -
164E PHE* 3.2 44.3 - - - +
167E GLU* 5.7 2.0 - - - -
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Residues in contact with LYS 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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143E GLN* 3.8 24.2 + - - +
146E ALA* 2.9 26.8 + - - +
147E ASN* 3.1 26.2 + - - +
149E ARG* 1.3 76.5 - - - +
151E VAL* 1.3 61.5 + - - +
152E ARG* 3.2 4.2 + - - -
153E LYS* 4.4 23.5 + - - +
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Residues in contact with VAL 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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105E MET* 4.4 9.4 - - + -
107E ILE* 3.5 24.0 - - + -
109E TYR* 3.8 20.9 + - + -
113E VAL* 3.9 36.1 - - + -
115E ILE* 4.6 13.0 - - + -
147E ASN 3.0 16.4 + - - +
148E VAL* 3.2 20.0 - - - +
149E ARG 3.0 0.8 + - - -
150E LYS* 1.3 76.2 - - - +
152E ARG* 1.3 59.5 + - - +
162E VAL* 4.6 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