Contacts of the strand formed by residues 133 - 151 (chain B) 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 GLY 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLY 3.4 9.6 - - - -
127A ASP* 4.4 1.3 - - - -
124B VAL* 3.6 6.9 - - - +
125B THR* 2.9 47.2 + - - +
131B LYS* 4.3 1.1 + - - -
132B ILE* 1.3 80.3 - - - +
134B GLY* 1.3 59.3 + - - -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL 4.5 0.2 - - - -
125A THR* 3.3 8.8 - - - +
126A GLY* 2.8 33.8 + - - +
123B ASN* 3.6 6.3 - - - -
124B VAL* 6.1 0.2 - - - -
125B THR* 5.5 0.7 - - - -
133B GLY* 1.3 74.4 - - - -
135B LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 2.8 46.9 - - - +
124A VAL 3.4 3.3 + - - -
125A THR* 3.3 14.8 - - + -
121B ASN* 5.2 9.0 - - - +
122B GLY* 3.0 8.1 - - - +
123B ASN* 2.9 71.1 + - + +
134B GLY* 1.3 75.1 - - - +
136B ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 3.5 4.0 - - - -
124A VAL* 2.8 45.7 + - + +
121B ASN 3.5 6.5 - - - +
122B GLY* 4.6 7.2 - - - -
135B LEU* 1.3 83.3 - - - +
137B GLY* 1.3 66.5 + - - +
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLY 3.2 15.3 - - - -
123A ASN* 3.5 11.0 + - - -
120B PHE* 3.5 3.5 - - - +
121B ASN* 2.9 44.5 + - - +
136B ILE* 1.3 80.5 - - - +
138B ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 3.3 3.1 - - - +
122A GLY* 2.9 32.0 + - - +
119B GLY 3.2 6.3 - - - -
120B PHE* 3.5 29.2 - - + +
121B ASN* 5.1 0.2 - - - -
137B GLY* 1.3 73.8 - - - -
139B ASN* 1.3 67.8 + - - +
140B VAL* 6.3 0.9 - - + -
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE 3.5 6.7 - - - +
121A ASN* 3.7 16.2 - - + +
117B THR* 4.6 4.7 - - - +
118B TYR* 3.4 2.9 - - - +
119B GLY* 2.8 55.8 + - - +
120B PHE* 4.4 1.1 - - - +
121B ASN* 4.6 9.9 + - - +
138B ALA* 1.3 80.7 - - - +
140B VAL* 1.3 73.9 + - - +
141B SER* 5.1 2.8 + - - -
141C SER* 5.2 3.4 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLY* 3.1 3.0 - - - -
120A PHE* 3.0 44.7 + - + +
116B LEU* 3.9 15.9 - - + -
117B THR 3.2 9.9 - - - +
118B TYR* 3.8 34.1 - - + +
138B ALA* 6.3 0.7 - - + -
139B ASN* 1.3 83.7 - - - +
141B SER* 1.3 64.5 + - - +
142B ILE* 5.1 3.8 - - + -
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 6.0 3.1 - - - -
118A TYR 3.6 9.9 - - - -
119A GLY* 4.0 3.4 - - - -
139A ASN* 6.0 0.7 - - - -
115B THR 3.7 0.6 - - - +
116B LEU* 3.4 7.4 - - - +
117B THR* 2.9 51.3 + - - -
139B ASN* 5.3 2.6 + - - -
140B VAL* 1.3 77.0 - - - +
142B ILE* 1.3 64.4 + - - +
143B GLY 4.2 0.7 - - - -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.3 3.8 - - - -
118A TYR* 2.9 72.7 + - + +
120A PHE* 6.3 2.5 - - + -
115B THR 3.3 7.2 - - - +
116B LEU* 3.5 24.5 - - + -
140B VAL* 5.1 3.8 - - + -
141B SER* 1.3 78.3 - - - +
143B GLY* 1.3 60.4 + - - +
144B HIS* 3.8 23.3 - - + +
179D TRP* 5.9 8.3 - - + -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 5.4 0.7 - - - -
116A LEU 3.3 7.4 - - - -
117A THR* 3.7 15.5 - - - -
113B ASN 4.4 0.2 - - - -
114B SER* 3.5 2.9 - - - -
115B THR* 2.8 40.2 + - - +
141B SER 4.2 0.2 - - - -
142B ILE* 1.3 75.0 - - - +
144B HIS* 1.3 68.0 + - - -
145B THR* 5.5 0.2 - - - -
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Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER 3.7 0.7 - - - +
115A THR* 3.3 3.3 - - - +
116A LEU* 2.9 46.6 + - + +
117A THR* 4.7 0.6 - - - +
118A TYR* 4.7 12.8 + + - -
112B TYR* 2.8 31.5 + - + +
113B ASN 3.1 5.8 - - - +
114B SER* 3.1 29.9 + - - -
142B ILE* 3.8 22.6 - - + +
143B GLY* 1.3 77.8 + - - -
145B THR* 1.3 62.8 + - - +
178D ASN* 5.2 5.6 - - + -
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Residues in contact with THR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 5.0 3.1 - - + -
114A SER 3.2 7.4 - - - +
115A THR* 2.8 30.3 + - - +
111B GLU 3.7 0.5 - - - +
112B TYR* 3.4 8.2 - - - -
113B ASN* 2.8 51.5 + - - +
143B GLY 5.5 0.2 - - - -
144B HIS* 1.3 77.1 + - - +
146B LEU* 1.3 71.0 + - - +
147B LYS* 3.9 28.0 - - + +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR 3.8 0.3 - - - +
113A ASN* 3.3 5.0 - - - -
114A SER* 2.8 40.2 + - - +
110B LYS* 3.7 29.6 - - + -
111B GLU 3.4 5.6 - - - +
112B TYR* 4.8 4.7 - - + +
145B THR* 1.3 74.4 - - - +
147B LYS* 1.3 68.5 + - - +
148B TYR* 3.3 31.6 - - + -
175C VAL* 3.8 18.6 - - + -
178C ASN 3.6 23.1 - - - +
179C TRP 4.8 2.9 - - - +
180C GLY 4.9 10.1 - - - +
181C PRO* 4.2 12.1 - - + -
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 4.3 9.3 + - - +
112A TYR 3.5 4.9 - - - -
113A ASN* 3.4 32.0 + - - +
147A LYS* 4.8 8.7 - - - +
110B LYS* 3.3 1.7 - - - +
111B GLU* 2.7 68.4 + - + +
113B ASN* 4.1 13.6 + - - +
145B THR* 3.9 19.5 - - + +
146B LEU* 1.3 78.9 - - - +
148B TYR* 1.3 66.4 + - - +
147C LYS* 5.2 7.9 - - - +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 4.5 3.6 - - - +
112A TYR* 2.9 50.2 + + + +
113A ASN* 4.6 0.4 - - - +
109B THR 4.0 8.3 - - - +
110B LYS* 3.7 16.4 - - + +
146B LEU* 3.3 38.1 - - + -
147B LYS* 1.3 80.7 - - - +
149B VAL* 1.3 68.0 + - - +
150B GLN* 3.3 34.3 - - + -
175C VAL* 4.1 15.0 - - + +
178C ASN* 2.4 40.8 + - - -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR* 3.9 27.1 - - + +
110A LYS 3.5 12.6 - - - +
111A GLU* 4.4 15.7 - - + +
109B THR 5.2 2.0 + - - +
148B TYR* 1.3 82.5 - - - +
150B GLN* 1.3 66.5 + - - +
151B PRO* 4.0 7.4 - - + +
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR* 4.4 1.3 - - - -
110A LYS* 2.8 56.4 + - + +
112A TYR* 3.2 33.7 - - + +
148B TYR* 3.3 35.2 + - + +
149B VAL* 1.3 79.3 - - - +
151B PRO* 1.3 59.4 - - - +
172B ASN* 4.0 6.5 + - - +
173B ASN* 3.1 34.3 + - - +
181B PRO* 3.9 11.7 - - - +
178C ASN* 4.4 6.3 + - - +
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Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE* 4.1 8.5 - - + -
108A ASP 3.6 6.7 - - - +
109A THR* 4.0 13.4 - - + -
110A LYS* 3.6 2.5 + - - -
149B VAL* 4.0 7.6 - - + +
150B GLN* 1.3 87.5 - - - +
152B ASP* 1.3 64.8 + - - +
153B PHE 3.2 23.1 - - - +
154B LYS* 4.2 14.1 - - + -
172B ASN* 3.1 26.9 + - - +
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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