Contacts of the helix formed by residues 116 - 131 (chain B) in PDB entry 3IHL
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 HIS 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A MET* 5.8 8.7 - - + -
114B VAL* 3.2 13.4 - - - +
115B PRO* 1.3 93.0 - - + +
117B ILE* 1.3 66.2 + - - +
118B THR* 3.2 4.3 - - - +
119B ASP* 3.3 30.9 + - + +
120B ALA 3.1 17.2 + - - -
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Residues in contact with ILE 117 (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 VAL* 4.2 6.4 + - + +
115B PRO 4.0 2.8 + - - -
116B HIS* 1.3 71.9 - - - +
118B THR* 1.3 60.5 + - - +
120B ALA* 3.2 10.7 + - + +
121B VAL* 2.8 41.6 + - + +
158B PRO* 3.8 28.0 - - + +
159B PHE* 3.9 31.2 - - + -
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Residues in contact with THR 118 (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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116B HIS* 3.2 5.1 - - - -
117B ILE* 1.3 87.3 - - - +
119B ASP* 1.3 65.7 + - - +
121B VAL* 3.7 2.5 + - - +
122B GLN* 3.0 46.1 + - - +
158B PRO* 3.6 18.9 + - - +
161B GLU* 4.2 9.5 - - - +
162B ALA* 4.0 12.8 - - - +
165B GLN* 3.4 27.1 - - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 5.9 0.4 - - + -
116B HIS* 3.3 33.5 + - + +
118B THR* 1.3 79.3 - - - +
120B ALA* 1.3 60.6 + - - +
122B GLN* 3.4 12.1 + - - +
123B GLU* 3.0 31.0 + - - +
165B GLN* 4.9 3.1 - - - +
169B LYS* 5.0 5.2 + - - -
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Residues in contact with ALA 120 (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 VAL* 3.7 30.9 - - + +
116B HIS 3.1 16.7 + - - +
117B ILE* 3.2 11.9 + - + +
119B ASP* 1.3 76.0 - - - +
121B VAL* 1.3 66.0 + - - +
123B GLU* 4.0 8.3 - - - +
124B TRP* 3.0 27.5 + - - +
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Residues in contact with VAL 121 (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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39B ILE* 3.8 27.1 - - + -
117B ILE* 2.8 26.4 + - + +
118B THR 3.9 0.7 - - - +
119B ASP 3.3 0.2 - - - -
120B ALA* 1.3 76.8 - - - +
122B GLN* 1.3 56.9 + - + +
124B TRP* 3.4 4.9 + - - +
125B VAL* 2.9 30.4 + - + +
159B PHE* 3.5 34.5 - - + -
162B ALA* 3.8 27.1 - - + -
163B PHE* 4.1 12.8 - - + -
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Residues in contact with GLN 122 (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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118B THR* 3.0 29.7 + - - +
119B ASP* 3.4 9.6 + - - +
120B ALA 3.4 0.4 - - - -
121B VAL* 1.3 74.8 - - + +
123B GLU* 1.3 64.6 + - - +
125B VAL* 4.6 2.7 - - - -
126B MET* 3.3 28.7 + - + +
162B ALA* 3.3 25.0 + - + +
163B PHE* 6.1 0.9 - - + -
165B GLN* 3.3 22.9 + - - +
166B PHE* 3.4 38.7 + - + -
169B LYS* 2.7 38.0 + - + +
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Residues in contact with GLU 123 (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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119B ASP 3.0 18.1 + - - +
120B ALA* 4.1 7.4 - - - +
122B GLN* 1.3 76.8 - - - +
124B TRP* 1.3 58.1 + - - +
126B MET* 3.4 6.4 + - - +
127B ASN* 3.1 49.9 + - - +
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Residues in contact with TRP 124 (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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37B ILE* 3.8 43.1 - - + -
38B LYS 4.3 11.4 - - - -
39B ILE* 4.3 16.8 - - + -
112B GLN* 6.0 4.0 - - - -
120B ALA 3.0 19.5 + - - +
121B VAL* 3.9 3.8 - - - +
123B GLU* 1.3 75.6 - - - +
125B VAL* 1.3 77.0 - - + +
127B ASN* 4.3 4.6 - - + +
128B GLN* 3.1 51.2 + - + +
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Residues in contact with VAL 125 (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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3B TYR* 4.0 16.4 - - + -
37B ILE* 4.1 15.0 - - + +
39B ILE* 3.9 21.3 - - + -
121B VAL* 2.9 21.4 + - + +
122B GLN* 4.2 5.2 - - - +
123B GLU 3.3 0.2 - - - -
124B TRP* 1.3 92.9 - - + +
126B MET* 1.3 64.2 + - - +
129B ALA* 3.1 24.3 + - - +
145B ILE* 3.9 23.1 - - + -
163B PHE* 4.2 12.8 - - + -
166B PHE* 4.1 10.3 - - + -
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Residues in contact with MET 126 (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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1B MET* 5.7 0.3 - - - +
3B TYR* 3.9 22.0 + - - +
122B GLN* 3.3 16.9 + - + +
123B GLU* 3.8 6.5 - - - +
124B TRP 3.4 0.2 - - - -
125B VAL* 1.3 81.1 - - - +
127B ASN* 1.3 65.1 + - - +
129B ALA* 3.8 4.2 + - - +
130B LYS* 3.8 32.8 + - - +
166B PHE* 3.8 23.8 - - + -
169B LYS* 5.4 12.6 - - + -
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Residues in contact with ASN 127 (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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123B GLU* 3.1 44.3 + - - +
124B TRP* 4.3 4.4 - - + +
126B MET* 1.3 80.1 - - - +
128B GLN* 1.3 65.6 + - + +
130B LYS* 3.2 32.1 + - - +
131B VAL* 3.7 8.7 + - - +
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Residues in contact with GLN 128 (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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35B THR* 4.9 5.2 + - - -
37B ILE* 4.2 20.8 - - + +
124B TRP* 3.1 55.8 + - + +
125B VAL 4.3 1.8 - - - +
127B ASN* 1.3 74.8 - - + +
129B ALA* 1.3 66.8 + - - +
131B VAL* 3.0 46.3 + - - +
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Residues in contact with ALA 129 (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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1B MET* 3.4 35.7 - - + +
3B TYR* 4.2 4.3 - - + -
35B THR* 3.9 10.7 - - - +
37B ILE* 4.9 1.0 - - - +
125B VAL 3.1 19.5 + - - +
126B MET 3.9 6.3 - - - +
128B GLN* 1.3 78.1 - - - +
130B LYS* 1.3 55.6 + - - +
140B PRO* 3.1 29.3 - - - +
143B CYS* 3.9 17.5 - - + -
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Residues in contact with LYS 130 (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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1B MET* 4.3 2.5 - - + -
126B MET* 3.8 28.7 + - - +
127B ASN* 3.2 22.0 + - - +
128B GLN 3.1 1.2 - - - -
129B ALA* 1.3 77.2 - - - +
131B VAL* 1.3 64.5 + - - +
132B PRO* 3.1 8.7 - - - +
139B GLU* 3.6 42.8 + - - +
140B PRO* 3.2 10.4 - - - +
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Residues in contact with VAL 131 (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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35B THR* 4.7 0.2 + - - -
127B ASN 3.8 10.1 - - - +
128B GLN* 3.0 41.8 + - - +
130B LYS* 1.3 75.3 - - - +
132B PRO* 1.3 81.0 - - + +
133B VAL* 3.4 14.9 - - + +
140B PRO* 3.7 7.5 - - - +
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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