Contacts of the strand formed by residues 140 - 152 (chain D) in PDB entry 2IVB
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 GLU 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LYS 4.7 1.4 - - - +
116A PHE* 3.9 21.4 - - + +
149A LYS* 3.5 11.2 - - - +
150A TYR* 3.0 52.2 + - + +
132D LYS* 3.1 31.3 - - + +
133D VAL 3.4 11.4 - - - +
134D ALA* 5.4 1.1 - - - -
135D ASP* 3.9 0.4 - - - +
138D GLY 4.2 0.2 + - - -
139D GLY* 1.3 80.1 - - - +
141D ARG* 1.3 64.8 + - - +
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Residues in contact with ARG 141 (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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116A PHE* 3.3 10.8 - - - -
125A ASN* 3.0 38.4 + - - -
126A PHE* 4.2 3.0 - - - +
127A LYS* 4.7 5.7 - - - +
147A ASP* 2.8 51.7 + - - +
148A GLY 3.4 7.6 - - - +
149A LYS* 3.8 12.4 - - - +
150A TYR 4.3 0.4 - - - +
131D LYS 3.7 0.2 - - - +
133D VAL* 2.8 42.4 + - + +
134D ALA 4.9 2.2 - - - -
135D ASP* 3.2 49.6 + - + +
136D PRO* 4.9 4.0 - - - -
140D GLU* 1.3 76.2 - - - +
142D ALA* 1.3 59.6 + - - +
143D VAL* 4.1 1.3 - - + -
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Residues in contact with ALA 142 (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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116A PHE* 3.5 14.7 - - + -
121A ILE* 3.4 38.8 - - + +
146A LEU 3.5 5.0 - - - +
147A ASP* 3.5 2.3 - - - +
148A GLY 2.8 29.8 + - - +
130D VAL* 4.9 3.6 - - + -
131D LYS 3.3 5.4 - - - +
141D ARG* 1.3 71.7 - - - +
143D VAL* 1.3 59.3 + - - +
144D ILE* 4.3 13.6 - - + +
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Residues in contact with VAL 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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145A THR* 3.6 24.9 - - + -
146A LEU 3.5 2.7 - - - -
147A ASP* 4.1 21.8 - - - +
129D ASP* 3.7 2.9 - - - +
131D LYS* 2.7 47.6 + - + +
133D VAL* 3.8 28.5 - - + -
141D ARG* 5.3 1.6 - - + -
142D ALA* 1.3 74.4 - - - +
144D ILE* 1.3 62.4 + - - +
145D THR* 4.0 11.3 + - - +
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Residues in contact with ILE 144 (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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108A LEU* 4.0 21.8 - - + -
112A VAL* 5.3 1.1 - - + -
121A ILE* 4.8 6.1 - - + -
144A ILE 3.6 1.4 - - - +
145A THR* 3.4 4.2 - - - +
146A LEU* 2.7 57.1 + - + +
97D PHE* 3.6 34.8 - - + -
100D MET* 5.9 0.2 - - + -
128D LEU* 4.7 2.7 - - + -
129D ASP 3.4 9.4 - - - +
130D VAL* 4.1 21.8 - - + -
142D ALA* 4.3 18.6 - - + +
143D VAL* 1.3 75.7 - - - +
145D THR* 1.3 63.1 + - - +
146D LEU* 4.1 18.6 + - + -
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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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143A VAL* 3.7 25.1 - - + -
144A ILE 3.6 3.1 - - - -
145A THR* 4.4 6.4 + - - +
127D LYS* 3.4 5.0 - - - +
128D LEU* 3.1 27.7 - - - +
129D ASP* 3.0 29.3 + - - +
143D VAL* 4.2 14.0 + - - +
144D ILE* 1.3 76.3 + - - +
146D LEU* 1.3 66.9 + - - +
147D ASP* 4.5 8.1 - - + +
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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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97A PHE* 5.1 11.0 - - + -
100A MET* 4.0 31.6 - - + -
142A ALA 3.6 2.9 - - - +
143A VAL* 3.4 1.6 - - - -
144A ILE* 2.8 59.7 + - + +
146A LEU* 4.1 18.8 - - + -
126D PHE* 3.4 34.3 - - + -
127D LYS 3.8 2.0 - - - -
128D LEU* 3.6 22.9 - - + -
144D ILE* 4.4 7.6 - - + -
145D THR* 1.3 75.8 - - - +
147D ASP* 1.3 59.7 + - - +
148D GLY 3.7 1.1 + - - -
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Residues in contact with ASP 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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133A VAL* 5.2 0.2 - - - +
141A ARG* 2.7 47.5 + - - +
142A ALA 3.8 2.2 - - - -
143A VAL* 3.9 19.5 - - + +
125D ASN 3.2 3.3 - - - +
126D PHE* 3.3 4.0 - - - -
127D LYS* 3.0 56.5 + - + +
145D THR* 4.6 10.1 - - + -
146D LEU* 1.3 71.6 - - - +
148D GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 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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141A ARG* 3.4 7.3 - - - -
142A ALA* 2.7 43.8 + - - +
121D ILE* 3.9 15.0 - - - +
122D ALA 4.3 1.3 - - - -
125D ASN 3.1 11.4 - - - -
126D PHE* 4.2 6.3 - - - -
146D LEU 3.7 2.0 + - - -
147D ASP* 1.3 74.7 + - - +
149D LYS* 1.3 61.7 + - - -
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Residues in contact with LYS 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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135A ASP* 3.1 23.8 - - + +
138A GLY 3.0 28.8 + - - -
139A GLY* 3.9 2.6 - - - -
140A GLU 3.7 23.1 - - - +
141A ARG* 3.9 5.7 - - - +
121D ILE* 4.5 1.8 - - - -
122D ALA* 2.9 28.0 + - - +
125D ASN* 3.6 35.4 + - + +
148D GLY* 1.3 73.7 - - - -
150D TYR* 1.3 73.7 + - - +
151D LEU* 3.5 16.0 + - + +
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Residues in contact with TYR 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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140A GLU* 2.7 45.8 + - + +
141A ARG* 4.4 0.2 - - - +
112D VAL* 5.1 1.1 - - + -
116D PHE* 3.3 56.8 + - + -
117D GLY* 3.3 15.9 - - - -
118D ASP 2.9 29.7 + - - -
119D GLY* 4.3 2.0 - - - -
120D ILE 3.4 18.2 - - - -
121D ILE* 3.8 11.3 - - + +
148D GLY 3.7 1.8 + - - -
149D LYS* 1.3 79.8 + - - +
151D LEU* 1.3 70.5 + - - +
152D PRO* 3.4 35.9 - - + +
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Residues in contact with LEU 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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122B ALA* 5.2 2.2 - - + -
124B ILE* 3.5 10.6 - - + +
125B ASN* 5.9 5.6 - - + +
151B LEU* 3.2 35.7 - - + -
119D GLY* 3.4 0.7 - - - -
120D ILE* 2.9 48.1 + - + -
122D ALA* 2.9 36.6 - - + -
125D ASN* 5.9 1.6 - - + +
149D LYS* 3.9 21.5 - - + +
150D TYR* 1.3 83.8 - - - +
152D PRO* 1.4 70.1 - - + +
1160F AZI 4.7 0.4 - - - +
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Residues in contact with PRO 152 (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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124B ILE* 3.4 14.2 - - - +
125B ASN* 4.8 3.6 + - - +
118D ASP 3.2 7.6 - - - +
150D TYR* 3.4 36.5 - - + +
151D LEU* 1.4 90.2 - - + +
153D THR* 1.3 59.7 - - - +
154D LYS* 3.4 39.6 + - + +
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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