Contacts of the strand formed by residues 132 - 151 (chain E) in PDB entry 3M4D
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 ILE 132 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ASP* 3.4 2.4 - - - -
128D ASP* 3.1 35.3 + - + +
124E VAL* 4.3 13.2 - - + -
125E THR 3.4 9.2 - - - +
126E GLY* 4.4 4.9 - - - -
127E ASP 5.9 1.1 - - - +
130E GLY* 3.6 13.0 - - - +
131E LYS* 1.3 89.0 - - - +
133E GLY* 1.3 67.5 + - - +
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Residues in contact with GLY 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D THR* 6.0 0.4 - - - -
126D GLY 3.3 10.5 - - - -
127D ASP* 4.1 5.4 - - - -
124E VAL* 3.3 12.5 - - - +
125E THR* 2.6 43.1 + - - +
131E LYS* 4.2 2.5 - - - +
132E ILE* 1.3 77.3 - - - +
134E GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D VAL 3.9 0.7 - - - +
125D THR* 3.3 7.9 - - - +
126D GLY* 2.8 37.5 + - - -
123E ASN* 3.0 11.0 - - - -
124E VAL* 4.3 1.8 - - - -
125E THR* 4.7 0.8 - - - -
133E GLY* 1.3 75.0 - - - -
135E LEU* 1.3 61.0 + - - -
136E ILE* 5.6 1.6 - - - -
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN* 3.0 42.4 - - - +
124D VAL 3.0 14.4 - - - +
125D THR* 2.9 31.0 - - + +
121E ASN* 3.8 7.2 - - - +
122E GLY* 3.2 5.2 - - - -
123E ASN* 2.6 65.2 + - + +
134E GLY* 1.3 74.1 - - - -
136E ILE* 1.3 67.3 + - - +
137E GLY 4.2 0.4 - - - +
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Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN* 3.5 4.3 + - - -
124D VAL* 2.9 44.9 + - + +
120E PHE* 6.5 0.2 - - + -
121E ASN 3.6 4.9 - - - +
122E GLY* 5.2 4.0 - - - -
123E ASN 5.6 0.2 - - - +
134E GLY 5.6 0.9 - - - -
135E LEU* 1.3 79.0 - - - +
137E GLY* 1.3 65.6 + - - +
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLY 3.7 13.5 - - - -
123D ASN* 4.3 5.8 - - - -
120E PHE* 3.2 6.8 - - - +
121E ASN* 2.8 49.7 + - - +
135E LEU 4.2 0.2 - - - -
136E ILE* 1.3 81.3 - - - +
138E ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ASN* 3.1 3.5 - - - +
122D GLY* 2.7 35.3 + - - +
119E GLY 3.2 11.7 - - - +
120E PHE* 4.1 5.8 - - + +
121E ASN* 3.9 0.8 + - - -
137E GLY* 1.3 75.9 - - - +
139E ASN* 1.3 64.0 + - - +
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Residues in contact with ASN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D PHE 3.2 14.1 - - - +
121D ASN* 3.6 11.3 - - + +
117E THR* 5.2 2.9 - - - +
118E TYR 4.4 1.2 - - - -
119E GLY* 2.7 54.0 + - - +
120E PHE 4.9 0.2 - - - +
121E ASN* 4.2 14.1 + - - -
138E ALA* 1.3 78.0 - - - +
140E VAL* 1.3 73.7 + - - +
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D GLY* 3.1 2.6 - - - -
120D PHE* 2.9 34.9 + - + +
116E LEU* 6.2 0.2 - - - -
117E THR 3.2 13.2 - - - +
118E TYR* 3.3 39.3 - - + -
139E ASN* 1.3 83.9 - - - +
141E SER* 1.3 70.2 + - - +
142E ILE* 5.2 7.4 - - + -
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Residues in contact with SER 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D THR* 4.4 13.7 - - - +
118D TYR 3.3 13.7 - - - -
119D GLY* 3.9 3.8 - - - -
139D ASN* 5.8 0.7 - - - -
115E THR 3.8 0.6 - - - +
116E LEU* 3.5 4.2 - - - -
117E THR* 3.0 46.2 + - - -
140E VAL* 1.3 78.8 - - - +
142E ILE* 1.3 66.7 + - - +
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Residues in contact with ILE 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D THR* 3.4 4.2 - - - -
118D TYR* 2.9 66.4 + - + +
115E THR 3.3 7.9 - - - +
116E LEU* 5.0 4.3 - - - -
140E VAL* 5.2 7.4 - - + -
141E SER* 1.3 80.3 - - - +
143E GLY* 1.3 62.0 + - - +
144E HIS* 3.6 28.0 - - + +
179G TRP* 5.4 16.8 - - + +
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Residues in contact with GLY 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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115D THR* 5.3 1.3 - - - -
116D LEU 3.3 8.3 - - - -
117D THR* 4.0 12.5 - - - +
113E ASN 4.4 0.7 - - - -
114E SER* 3.5 0.2 - - - -
115E THR* 2.8 41.6 + - - +
142E ILE* 1.3 75.5 - - - +
144E HIS* 1.3 71.4 + - - -
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Residues in contact with HIS 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D SER 3.8 1.0 - - - +
115D THR* 3.2 5.6 - - - +
116D LEU* 2.9 47.0 + - + +
118D TYR* 4.8 12.3 + + - -
112E TYR* 3.5 31.7 + + + +
113E ASN 3.3 3.4 - - - -
114E SER* 3.3 29.1 + - - -
142E ILE* 3.6 23.3 - - + +
143E GLY* 1.3 78.9 + - - -
145E THR* 1.3 61.9 + - - +
178G ASN* 5.2 6.5 - - + -
179G TRP* 6.2 6.4 - + - -
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Residues in contact with THR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D ASN* 4.6 6.1 - - + -
114D SER 3.4 4.5 - - - +
115D THR* 2.7 32.8 + - - +
111E GLU 3.7 0.9 - - - +
112E TYR* 3.4 10.5 - - - -
113E ASN* 2.9 45.1 + - - +
144E HIS* 1.3 74.9 + - - +
146E LEU* 1.3 64.0 + - - +
147E LYS* 3.8 33.0 - - + -
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Residues in contact with LEU 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D TYR 3.8 0.5 - - - +
113D ASN* 3.1 7.3 - - - +
114D SER* 2.9 36.9 + - - +
110E LYS* 4.2 13.5 - - + -
111E GLU 3.5 11.4 - - - +
112E TYR* 4.3 9.6 - - + -
145E THR* 1.3 72.5 - - - +
147E LYS* 1.3 61.1 + - - +
148E TYR* 3.6 25.7 - - + -
175F VAL* 3.8 31.6 - - + -
178F ASN 3.7 22.2 - - - +
179F TRP 4.5 3.8 - - - +
180F GLY 4.6 8.3 - - - +
181F PRO* 4.1 16.6 - - + -
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Residues in contact with LYS 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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111D GLU* 4.3 8.9 + - - +
113D ASN* 3.6 33.7 + - - +
147D LYS* 4.8 9.7 - - - +
110E LYS* 3.6 1.2 - - - +
111E GLU* 2.8 69.1 + - + +
113E ASN* 3.9 16.7 + - - +
145E THR* 3.8 17.0 - - + +
146E LEU* 1.3 78.5 - - - +
148E TYR* 1.3 64.4 + - - +
147F LYS* 5.1 8.1 - - - +
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Residues in contact with TYR 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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111D GLU* 4.5 3.9 - - - +
112D TYR* 3.1 54.3 + + - +
113D ASN* 4.1 1.2 - - - +
109E THR 4.2 16.8 - - - +
110E LYS* 4.2 7.0 - - + +
146E LEU* 3.6 33.9 - - + -
147E LYS* 1.3 79.6 - - - +
149E VAL* 1.3 66.8 + - - +
150E GLN* 3.1 32.1 + - + -
175F VAL* 4.1 18.6 - - + -
178F ASN* 2.4 44.4 + - - -
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Residues in contact with VAL 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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109D THR* 3.9 26.9 - - + +
110D LYS 3.6 12.8 - - - +
111D GLU* 4.4 15.5 - - + +
109E THR 5.3 2.0 + - - +
148E TYR* 1.3 80.3 - - - +
150E GLN* 1.3 66.8 + - - +
151E PRO* 3.9 8.2 - - + +
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Residues in contact with GLN 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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109D THR* 4.4 0.9 - - - -
110D LYS* 2.8 48.5 + - - +
112D TYR* 3.4 23.9 - - - +
148E TYR* 3.1 40.8 + - + +
149E VAL* 1.3 78.8 - - - +
151E PRO* 1.3 63.5 - - - +
172E ASN* 4.2 4.7 - - - +
173E ASN* 3.4 33.9 + - - +
181E PRO* 3.8 17.2 - - - +
178F ASN* 3.8 8.7 + - - +
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Residues in contact with PRO 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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107D ILE* 4.2 4.7 - - + -
108D ASP 3.6 6.5 - - - +
109D THR* 3.9 16.8 - - + -
110D LYS* 3.6 2.1 + - - -
149E VAL* 3.9 8.1 - - + +
150E GLN* 1.3 85.8 - - - +
152E ASP* 1.3 65.1 + - - +
153E PHE 3.4 20.2 - - - +
154E LYS* 4.1 17.3 - - + -
172E ASN* 2.9 29.1 + - - +
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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
------------------------------------------------------------
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