Contacts of the strand formed by residues 109 - 126 (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 THR 109 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ILE 3.9 9.6 - - - +
108E ASP* 1.3 84.6 - - - +
110E LYS* 1.3 65.6 + - - +
148E TYR* 4.2 11.1 - - - +
149E VAL 5.3 1.4 + - - +
149F VAL* 3.8 22.8 - - + +
150F GLN 3.7 7.2 - - - -
151F PRO* 3.8 17.7 - - + -
152F ASP* 4.6 0.9 - - - +
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Residues in contact with LYS 110 (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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109E THR* 1.3 76.3 - - - +
111E GLU* 1.3 61.5 + - - +
146E LEU* 4.2 13.5 - - + -
147E LYS 3.6 10.8 - - - +
148E TYR* 4.2 7.2 - - + -
149F VAL* 3.4 5.8 - - - +
150F GLN* 2.7 60.8 + - + +
151F PRO 3.7 2.2 - - - -
152F ASP* 2.8 29.5 + - - -
173F ASN* 2.7 35.3 + - - +
175F VAL* 3.5 33.2 - - + +
181F PRO* 3.8 13.7 - - + -
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Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LYS* 1.3 73.9 - - - +
112E TYR* 1.3 62.0 + - - +
113E ASN* 3.4 29.4 + - - +
145E THR 3.7 0.3 - - - +
146E LEU* 3.5 8.3 - - - +
147E LYS* 2.8 62.9 + - + +
147F LYS* 4.4 11.1 + - - +
148F TYR 3.7 15.7 - - - +
149F VAL* 4.4 14.1 - - + +
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Residues in contact with TYR 112 (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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110E LYS 4.2 0.4 + - - -
111E GLU* 1.3 72.5 - - - +
113E ASN* 1.3 72.2 + - - +
114E SER* 3.8 18.8 - - - -
144E HIS* 3.5 35.1 + - + +
145E THR 3.4 17.5 - - - -
146E LEU* 4.3 9.6 - - + -
146F LEU 3.8 0.5 - - - +
147F LYS* 3.6 1.4 - - - -
148F TYR* 3.2 34.2 + - + +
150F GLN* 4.0 24.4 - - - +
180F GLY 3.8 23.6 + - - -
181F PRO* 3.8 16.8 - - + -
178G ASN* 3.0 41.5 + - - -
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Residues in contact with ASN 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E GLU* 3.4 31.1 + - - +
112E TYR* 1.3 98.7 + - - +
114E SER* 1.3 62.9 + - - +
115E THR* 5.0 1.6 - - - +
143E GLY 3.9 0.3 - - - +
144E HIS* 3.3 6.2 + - - +
145E THR* 2.9 47.8 + - - +
147E LYS* 3.9 17.7 - - - -
145F THR* 4.6 7.0 - - + -
146F LEU 3.1 6.7 - - - +
147F LYS* 3.5 34.1 - - + +
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Residues in contact with SER 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E TYR* 3.8 13.6 - - - -
113E ASN* 1.3 72.5 - - - +
115E THR* 1.3 62.6 + - - +
143E GLY 3.5 4.5 - - - -
144E HIS* 3.3 25.4 + - - -
144F HIS 3.7 0.9 - - - +
145F THR* 3.3 2.1 - - - -
146F LEU* 2.8 46.0 + - - +
148F TYR* 5.0 1.1 + - - -
178G ASN* 3.4 25.1 + - - +
179G TRP* 6.4 0.2 - - - -
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Residues in contact with THR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ASN* 5.0 2.3 - - - +
114E SER* 1.3 75.1 + - - +
116E LEU* 1.3 61.6 + - - +
117E THR* 3.7 18.6 - - - +
141E SER* 3.8 0.7 - - - +
142E ILE* 3.3 8.3 - - - +
143E GLY* 2.8 46.3 + - - +
143F GLY* 5.6 0.7 - - - -
144F HIS 3.3 7.6 - - - +
145F THR* 2.9 31.5 + - - +
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR* 1.3 74.5 - - - +
117E THR* 1.3 62.5 + - - +
118E TYR* 4.9 9.4 - - - -
140E VAL* 6.2 0.4 - - - -
141E SER 3.5 5.6 - - - -
142E ILE* 4.7 5.8 - - - +
142F ILE 3.9 0.7 - - - +
143F GLY* 3.3 1.7 - - - -
144F HIS* 2.9 38.6 + - - +
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Residues in contact with THR 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E THR* 3.7 15.8 - - - +
116E LEU* 1.3 77.4 + - - +
118E TYR* 1.3 74.8 + - - +
139E ASN* 4.6 3.0 - - - +
140E VAL* 3.2 8.6 - - - +
141E SER* 3.0 45.3 + - - -
141F SER* 4.4 11.9 - - - +
142F ILE 3.4 14.1 - - - +
143F GLY* 4.0 6.0 - - - -
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Residues in contact with TYR 118 (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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116E LEU* 4.9 8.5 - - - -
117E THR* 1.3 79.3 - - - +
119E GLY* 1.3 59.0 + - - +
120E PHE* 5.7 0.2 - - - -
139E ASN* 3.5 4.9 - - - +
140E VAL* 3.3 37.2 - - + +
141F SER* 3.0 7.0 - - - -
142F ILE* 2.8 47.2 + - + +
144F HIS* 5.8 7.2 - + - -
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Residues in contact with GLY 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR* 1.3 78.7 - - - +
120E PHE* 1.3 64.8 + - - +
138E ALA* 3.2 5.3 - - - +
139E ASN* 2.7 52.4 + - - +
140F VAL 3.2 11.2 - - - -
141F SER* 3.9 5.4 - - - -
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Residues in contact with PHE 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E TYR 5.7 0.4 - - - -
119E GLY* 1.3 79.0 - - - +
121E ASN* 1.3 64.1 + - - +
136E ILE* 6.5 0.2 - - + -
137E GLY 3.2 12.3 - - - +
138E ALA* 4.1 5.8 - - + +
139E ASN* 5.6 0.2 - - - -
139F ASN* 3.3 3.0 - - - +
140F VAL* 2.9 77.3 + - + -
141F SER* 4.8 1.1 - - - -
142F ILE* 6.0 4.0 - - + -
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Residues in contact with ASN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASN* 5.1 5.3 + - - -
120E PHE* 1.3 79.7 - - - +
122E GLY* 1.3 65.4 + - - +
123E ASN* 5.5 1.8 - - - +
135E LEU* 3.8 7.3 - - - +
136E ILE* 3.6 3.9 - - - +
137E GLY* 2.8 55.9 + - - +
138E ALA 3.9 0.5 + - - -
139E ASN* 4.2 11.2 + - - -
138F ALA 3.3 13.2 - - - +
139F ASN* 3.6 11.9 - - + +
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Residues in contact with GLY 122 (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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120E PHE* 6.0 0.2 - - - -
121E ASN* 1.3 77.6 + - - +
123E ASN* 1.3 66.9 + - - +
135E LEU 3.2 6.5 - - - -
136E ILE* 4.7 6.3 - - - -
137F GLY* 3.5 2.6 - - - -
138F ALA* 2.9 32.1 + - - +
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Residues in contact with ASN 123 (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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121E ASN* 5.5 2.9 - - - +
122E GLY* 1.3 74.7 - - - +
124E VAL* 1.3 66.9 + - - +
125E THR* 3.4 11.3 + - - -
134E GLY* 3.0 4.5 - - - -
135E LEU* 2.6 66.3 + - + +
121F ASN* 5.8 0.9 + - - -
135F LEU* 3.0 38.0 - - - +
136F ILE 3.3 16.1 - - - +
137F GLY* 3.9 3.2 - - - -
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Residues in contact with VAL 124 (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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123E ASN* 1.3 81.2 - - - +
125E THR* 1.3 67.7 + - - +
132E ILE* 4.3 14.8 - - + -
133E GLY 3.3 15.0 - - - +
134E GLY* 5.1 1.6 - - - -
134F GLY 4.9 0.2 - - - -
135F LEU* 3.6 2.8 - - - +
136F ILE* 2.8 44.5 + - + +
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Residues in contact with THR 125 (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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123E ASN* 3.4 10.0 + - - -
124E VAL* 1.3 75.7 - - - +
126E GLY* 1.3 71.3 + - - +
132E ILE* 3.4 7.3 - - - +
133E GLY* 2.6 44.1 + - - +
134E GLY 5.3 0.2 + - - -
134F GLY 3.5 15.0 - - - +
135F LEU* 3.0 21.1 - - + +
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Residues in contact with GLY 126 (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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125E THR* 1.3 85.3 - - - +
127E ASP* 1.3 59.7 + - - -
131E LYS* 3.0 15.0 - - - -
132E ILE* 4.4 6.7 - - - -
133F GLY* 3.3 1.0 - - - -
134F GLY* 2.5 40.1 + - - +
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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
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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