Contacts of the strand formed by residues 132 - 151 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127C ASP 3.6 0.9 - - - -
128C ASP* 2.8 40.7 + - + +
124D VAL* 4.6 10.3 - - + -
125D THR 3.6 7.0 - - - +
126D GLY* 4.1 11.7 - - - -
127D ASP 5.1 1.8 - - - +
130D GLY* 3.5 14.8 - - - +
131D LYS* 1.3 80.4 - - - +
133D GLY* 1.3 63.9 + - - +
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLY 3.4 13.0 - - - -
127C ASP* 3.9 6.3 - - - -
124D VAL* 3.3 9.4 - - - +
125D THR* 2.6 47.5 + - - +
131D LYS* 4.0 4.1 - - - +
132D ILE* 1.3 76.3 - - - +
134D GLY* 1.3 55.3 + - - -
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C THR* 3.7 3.8 - - - +
126C GLY* 3.0 32.1 + - - +
123D ASN* 3.0 12.1 - - - -
124D VAL* 4.0 7.6 - - - -
125D THR* 5.7 0.7 - - - -
133D GLY* 1.3 75.3 - - - -
135D LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASN* 2.9 49.4 - - - +
124C VAL 3.0 23.3 - - - +
125C THR* 3.3 13.7 - - + -
121D ASN* 5.3 6.5 - - - +
122D GLY* 3.2 6.6 - - - -
123D ASN* 2.7 62.3 + - + +
124D VAL* 5.6 0.2 - - - +
134D GLY* 1.3 75.2 - - - +
136D ILE* 1.3 73.4 + - - +
137D GLY 4.8 0.7 - - - +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASN* 3.8 0.2 - - - -
124C VAL* 3.0 34.3 + - + +
120D PHE* 5.1 10.8 - - + -
121D ASN 3.4 8.1 - - - +
122D GLY* 5.0 3.6 - - - -
135D LEU* 1.3 88.1 - - - +
137D GLY* 1.3 66.8 + - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLY 3.4 14.8 - - - -
123C ASN* 3.8 9.9 + - - -
120D PHE* 3.2 11.8 - - - -
121D ASN* 3.0 43.8 + - - +
135D LEU 4.3 0.2 - - - -
136D ILE* 1.3 75.7 - - - +
138D ALA* 1.3 59.6 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASN* 3.2 3.3 - - - +
122C GLY* 2.9 32.7 + - - +
119D GLY 3.4 7.9 - - - +
120D PHE* 3.3 30.3 - - + -
137D GLY* 1.3 71.4 - - - -
139D ASN* 1.3 68.7 + - - +
140D VAL* 6.3 0.7 - - + -
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C PHE 3.3 7.0 - - - +
121C ASN* 3.5 17.1 - - + +
117D THR* 5.7 0.7 - - - +
118D TYR* 3.0 6.2 - - - +
119D GLY* 2.9 38.8 + - - +
120D PHE* 5.4 0.4 - - - +
121D ASN* 4.1 16.4 + - - -
138D ALA* 1.3 82.2 - - - +
140D VAL* 1.3 67.7 + - - +
141E SER* 5.8 0.7 - - - -
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY* 3.2 1.7 - - - -
120C PHE* 2.9 43.5 + - + +
116D LEU* 4.0 20.6 - - + -
117D THR 3.2 9.6 - - - +
118D TYR* 3.6 14.4 - - + -
138D ALA* 6.3 0.2 - - + -
139D ASN* 1.3 81.9 - - - +
141D SER* 1.3 65.6 + - - +
142D ILE* 5.0 5.4 - - + -
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Residues in contact with SER 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR* 4.6 11.5 - - - +
118C TYR 3.3 13.0 - - - -
119C GLY* 4.1 5.6 - - - -
139C ASN* 5.8 0.9 - - - -
115D THR 3.8 0.9 - - - +
116D LEU* 3.5 4.5 - - - +
117D THR* 2.7 52.7 + - - +
140D VAL* 1.3 77.5 - - - +
142D ILE* 1.3 63.8 + - - +
143D GLY 4.3 0.2 - - - -
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR* 4.2 2.5 - - - -
118C TYR* 2.9 75.0 + - + +
120C PHE* 6.4 1.1 - - + -
114D SER* 6.1 2.9 - - - -
115D THR 3.3 9.9 - - - +
116D LEU* 3.5 28.7 - - + -
140D VAL* 5.0 4.7 - - + -
141D SER* 1.3 73.1 - - - +
143D GLY* 1.3 64.8 + - - +
144D HIS* 6.3 0.4 - - + -
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Residues in contact with GLY 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C THR* 5.4 2.0 - - - -
116C LEU 3.1 12.1 - - - -
117C THR* 4.0 13.0 - - - +
118C TYR* 5.0 0.9 - - - -
113D ASN 4.0 0.2 - - - +
114D SER* 3.4 2.6 - - - -
115D THR* 2.7 44.1 + - - -
142D ILE* 1.3 80.0 - - - +
144D HIS* 1.3 59.8 + - - +
145D THR* 5.5 0.2 - - - -
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Residues in contact with HIS 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C SER 3.8 1.1 - - - +
115C THR* 3.3 3.4 - - - +
116C LEU* 3.0 75.6 + - + +
118C TYR* 5.3 6.7 - + - -
112D TYR* 3.0 42.8 - + + +
113D ASN 3.0 9.9 - - - +
114D SER* 4.4 2.2 - - - -
142D ILE* 6.3 0.4 - - + -
143D GLY* 1.3 76.0 - - - +
145D THR* 1.3 64.5 + - - +
146D LEU* 5.5 2.7 - - + -
180E GLY 4.4 13.6 + - - -
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Residues in contact with THR 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASN* 4.6 5.2 - - + -
114C SER 3.1 8.7 - - - +
115C THR* 2.6 33.8 + - - +
111D GLU 3.7 0.9 - - - +
112D TYR* 3.5 7.8 - - - -
113D ASN* 2.7 46.8 + - - +
143D GLY 5.5 0.2 - - - -
144D HIS* 1.3 74.5 - - - +
146D LEU* 1.3 70.1 + - - +
147D LYS* 3.9 26.0 - - + -
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C TYR 3.7 1.0 - - - +
113C ASN* 3.1 6.1 - - - -
114C SER* 2.8 38.6 + - - +
110D LYS* 3.9 14.6 - - + -
111D GLU 3.5 9.0 - - - +
112D TYR* 4.8 5.2 - - + +
144D HIS* 5.5 3.3 - - + -
145D THR* 1.3 74.0 - - - +
147D LYS* 1.3 65.0 + - - +
148D TYR* 3.5 27.8 - - + -
175E VAL* 3.8 30.5 - - + -
178E ASN 3.5 23.8 - - - +
179E TRP 4.5 3.4 - - - +
180E GLY 4.6 11.7 - - - +
181E PRO* 4.4 13.2 - - + -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLU* 4.0 11.8 + - - +
112C TYR 3.5 3.8 - - - -
113C ASN* 3.5 30.5 - - - +
147C LYS* 5.2 6.9 - - - +
110D LYS* 3.4 1.2 - - - +
111D GLU* 2.7 75.5 + - + +
113D ASN* 3.9 16.0 + - - +
145D THR* 3.9 15.7 - - + +
146D LEU* 1.3 77.6 - - - +
148D TYR* 1.3 66.3 + - - +
147E LYS* 4.8 9.9 - - - +
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Residues in contact with TYR 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLU* 4.4 4.1 - - - +
112C TYR* 3.0 48.3 + + + +
113C ASN* 4.3 0.8 - - - +
114C SER* 5.3 0.7 - - - -
109D THR 4.1 6.3 - - - +
110D LYS* 3.7 19.1 - - + +
146D LEU* 3.5 38.6 - - + -
147D LYS* 1.3 80.1 - - - +
149D VAL* 1.3 67.6 + - - +
150D GLN* 2.8 33.9 + - + -
175E VAL* 4.2 14.6 - - + -
178E ASN* 2.3 42.5 + - - -
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C THR* 3.7 28.0 - - + +
110C LYS 3.5 13.5 - - - +
111C GLU* 4.4 15.3 - - + +
109D THR 5.3 2.1 + - - +
148D TYR* 1.3 80.1 - - - +
150D GLN* 1.3 67.3 + - - +
151D PRO* 3.9 8.3 - - + +
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Residues in contact with GLN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C THR* 4.4 1.1 - - - -
110C LYS* 2.8 46.1 + - - +
112C TYR* 3.7 21.2 - - - +
148D TYR* 2.8 40.6 + - + +
149D VAL* 1.3 79.1 - - - +
151D PRO* 1.3 64.5 - - - +
172D ASN* 4.1 5.8 - - - +
173D ASN* 3.6 36.1 + - - +
181D PRO* 4.1 15.2 - - - +
178E ASN* 3.7 9.4 + - - -
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Residues in contact with PRO 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 4.1 5.4 - - + -
108C ASP 3.6 6.3 - - - +
109C THR* 3.7 19.5 - - + -
110C LYS* 3.5 2.2 + - - -
149D VAL* 3.9 8.1 - - + +
150D GLN* 1.3 86.2 - - - +
152D ASP* 1.3 65.0 + - - +
153D PHE 3.3 22.7 - - - +
154D LYS* 4.3 13.5 - - + -
172D ASN* 2.9 31.1 + - - +
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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