Contacts of the helix formed by residues 131 - 149 (chain B) in PDB entry 1IBL
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 PRO 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 1.3 104.6 - - + +
132B LYS* 1.3 59.9 + - - +
133B LYS* 2.8 46.8 + - + +
134B GLU* 3.1 13.0 + - - +
135B GLN* 3.0 11.7 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1160A G 6.2 3.6 - - - -
131B PRO* 1.3 69.6 - - - +
133B LYS* 1.3 65.8 + - - +
134B GLU 3.1 0.4 - - - -
135B GLN* 3.0 36.7 + - + +
136B VAL* 3.0 37.7 - - + +
139B LYS* 5.2 8.2 - - - +
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Residues in contact with LYS 133 (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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1111A A 4.2 29.9 + - - +
1112A C 5.2 2.6 + - - -
1158A C 4.8 26.0 + - - +
131B PRO* 2.8 30.9 + - + +
132B LYS* 1.3 79.6 - - - +
134B GLU* 1.3 62.9 + - + +
136B VAL* 4.3 1.7 - - - +
137B ARG* 2.8 27.7 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 2.9 56.4 + - + +
131B PRO* 3.1 10.8 + - - +
133B LYS* 1.3 77.7 - - + +
135B GLN* 1.3 54.4 + - - +
136B VAL 2.6 17.6 + - - -
137B ARG* 3.1 43.1 + - - +
138B LEU* 3.0 32.4 + - + +
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Residues in contact with GLN 135 (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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122B PHE* 6.0 1.8 - - + -
127B ILE* 2.7 30.2 + - + +
128B GLU* 3.3 22.2 - - - +
129B GLU 4.6 4.4 + - - +
130B ARG 3.8 10.0 + - - +
131B PRO* 3.0 7.9 + - - +
132B LYS* 3.0 45.8 + - - +
134B GLU* 1.3 74.9 - - - +
136B VAL* 1.3 61.1 + - - +
138B LEU* 5.1 3.8 - - - -
139B LYS* 2.8 41.3 - - + +
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Residues in contact with VAL 136 (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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132B LYS* 3.0 31.0 - - + +
133B LYS 4.3 2.0 - - - +
134B GLU 2.6 7.5 + - - -
135B GLN* 1.3 84.5 - - - +
137B ARG* 1.3 59.1 + - + +
138B LEU 2.8 5.6 - - - +
139B LYS* 3.4 17.0 - - + +
140B HIS* 2.8 49.7 + - + +
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Residues in contact with ARG 137 (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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1110A A 6.3 0.6 - - - -
133B LYS* 2.8 26.9 - - - +
134B GLU* 3.1 43.9 + - - +
136B VAL* 1.3 78.8 - - + +
138B LEU* 1.3 67.2 + - + +
140B HIS* 4.8 1.9 - - - +
141B GLU* 2.9 26.9 + - - +
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Residues in contact with LEU 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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114B ARG* 4.5 21.1 - - - +
118B LEU* 3.9 23.2 - - + +
121B LEU* 4.7 17.0 - - + -
122B PHE* 4.2 13.7 - - + -
134B GLU* 3.0 23.8 - - + +
135B GLN* 5.1 2.0 - - - -
136B VAL 2.8 0.6 - - - +
137B ARG* 1.3 95.0 - - + +
139B LYS* 1.3 66.7 + - - +
140B HIS 2.8 3.7 + - - -
141B GLU* 2.8 18.3 + - - +
142B LEU* 2.9 16.6 + - - +
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Residues in contact with LYS 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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122B PHE* 3.5 37.3 - - + -
127B ILE* 4.7 10.1 - - - +
132B LYS* 5.2 10.3 - - - +
135B GLN* 2.8 47.0 - - - +
136B VAL* 3.4 18.8 - - + +
138B LEU* 1.3 78.8 - - - +
140B HIS* 1.3 53.4 + - + +
142B LEU* 4.5 2.1 - - - +
143B GLU* 2.7 38.3 + - - +
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Residues in contact with HIS 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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1169A A 5.5 5.3 + - - -
136B VAL* 2.8 30.6 + - + +
137B ARG* 4.8 1.8 - - - +
138B LEU 2.8 0.2 + - - -
139B LYS* 1.3 79.2 - - + +
141B GLU* 1.3 65.5 + - - +
142B LEU 3.0 1.8 - - - -
143B GLU* 2.8 33.1 + - + +
144B ARG* 2.9 15.2 + - - +
147B LYS* 5.6 3.7 + - - -
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Residues in contact with GLU 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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111B ARG* 4.9 11.5 + - - +
114B ARG* 2.8 53.6 + - - -
118B LEU* 3.4 4.6 - - + +
137B ARG 2.9 24.7 + - - +
138B LEU* 2.8 11.7 + - - +
140B HIS* 1.3 76.3 - - - +
142B LEU* 1.3 56.1 + - - +
144B ARG* 3.0 16.4 - - + +
145B LEU* 2.8 31.7 - - + +
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Residues in contact with LEU 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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115B LEU* 3.7 14.1 - - + -
118B LEU* 3.4 24.0 - - + +
119B GLU* 3.2 37.7 - - + +
122B PHE* 4.9 16.2 - - + -
138B LEU 2.9 10.2 + - - +
139B LYS 4.5 3.4 - - - +
141B GLU* 1.3 77.2 - - - +
143B GLU* 1.3 72.1 + - - +
144B ARG 3.1 0.6 + - - -
145B LEU* 3.2 5.6 + - - +
146B GLN* 2.9 55.6 + - + +
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Residues in contact with GLU 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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122B PHE* 5.9 1.2 - - - -
139B LYS 2.7 27.7 - - - +
140B HIS* 2.8 35.3 + - + +
142B LEU* 1.3 86.8 - - - +
144B ARG* 1.3 59.8 + - - +
146B GLN* 3.7 5.9 + - - +
147B LYS* 2.9 36.6 + - - +
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Residues in contact with ARG 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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1100A C 5.5 5.3 - - - +
1103A C 4.2 12.3 + - - -
1104A G 3.0 34.7 + - - -
98B LEU* 5.0 9.5 - - - +
111B ARG* 5.0 1.4 - - - +
140B HIS 2.9 9.6 + - - +
141B GLU* 3.0 22.9 - - + +
143B GLU* 1.3 74.8 - - - +
145B LEU* 1.3 87.7 + - + +
147B LYS* 2.5 53.6 + - + +
148B TYR* 3.2 37.9 + - + +
149B LEU* 5.9 2.4 - - - +
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Residues in contact with LEU 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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111B ARG* 4.6 20.4 - - - +
114B ARG* 4.4 7.0 - - + -
115B LEU* 3.5 48.9 - - + +
118B LEU* 4.3 7.9 - - + -
141B GLU* 2.8 28.5 - - + +
142B LEU* 3.2 12.5 + - - +
144B ARG* 1.3 103.0 - - - +
146B GLN* 1.3 54.0 + - - +
147B LYS 2.6 11.6 + - - -
148B TYR* 2.9 2.4 + - - +
149B LEU* 2.8 46.2 + - + +
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Residues in contact with GLN 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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115B LEU* 3.8 14.6 - - + +
119B GLU* 3.5 18.9 + - - +
142B LEU* 2.9 39.4 + - + +
143B GLU* 4.0 6.3 - - - +
145B LEU* 1.3 78.2 - - - +
147B LYS* 1.3 56.6 + - - +
150B SER* 3.0 31.0 - - - +
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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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1098A C 4.7 12.7 + - - -
95B GLN* 3.4 29.2 + - + +
140B HIS* 5.6 3.2 + - - -
143B GLU* 2.9 36.1 - - - +
144B ARG* 2.5 35.9 + - + +
145B LEU 2.6 0.4 + - - -
146B GLN* 1.3 74.8 - - - +
148B TYR* 1.3 76.4 + - + +
150B SER* 4.0 7.6 + - - -
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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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1099A G 3.7 22.9 + - - -
1100A C 5.7 0.9 + - - -
92B TYR 5.2 1.7 - - - +
93B VAL* 5.5 8.1 - - - +
94B ASN 5.8 0.9 + - - -
95B GLN* 3.8 39.1 + - + +
96B ARG* 4.4 23.3 - - + +
98B LEU* 4.6 22.4 - - + -
101B MET* 5.2 2.9 - - + +
144B ARG* 3.8 51.6 - - + +
145B LEU* 2.9 4.1 + - - +
147B LYS* 1.3 87.5 - - + +
149B LEU* 1.3 68.4 + - + +
150B SER* 3.0 12.2 + - - -
151B GLY 4.4 2.6 + - - -
152B PHE* 4.5 6.1 + - - +
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Residues in contact with LEU 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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98B LEU* 4.1 14.1 - - + -
101B MET* 3.9 27.1 - - + -
108B ILE* 4.5 5.8 - - + +
111B ARG* 3.3 35.4 - - + +
112B VAL* 3.8 20.9 - - + +
115B LEU* 3.7 16.8 - - + +
144B ARG* 5.9 3.1 - - - +
145B LEU* 2.8 34.2 + - + +
148B TYR* 1.3 74.1 - - + +
150B SER* 1.3 60.6 + - - -
151B GLY 3.4 1.6 - - - -
152B PHE* 4.0 20.2 - - + -
153B ARG* 3.5 16.9 - - - +
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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