Contacts of the helix formed by residues 110 - 123 (chain B) in PDB entry 3IEQ
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 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B VAL* 4.2 18.2 - - + -
26B THR 5.3 1.6 - - - -
27B ILE* 3.8 39.5 - - + +
28B PRO* 4.9 9.2 - - + +
106B LYS 3.7 19.4 + - - -
107B LEU* 2.8 19.1 + - - +
109B PRO* 1.3 87.8 - - + +
111B ILE* 1.3 62.8 + - - +
112B ASP 3.5 1.8 - - - -
113B ALA* 3.4 9.7 + - - +
114B MET* 3.1 39.9 + - + +
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Residues in contact with ILE 111 (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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58A ASP* 5.9 0.7 - - - +
100B ILE* 4.8 1.1 - - + -
107B LEU* 3.6 15.7 - - + +
108B ALA* 3.3 25.1 + - - +
109B PRO 3.4 0.4 - - - -
110B HIS* 1.3 77.9 - - - +
112B ASP* 1.3 62.0 + - - +
114B MET* 3.4 13.8 + - - +
115B ARG* 2.9 44.0 + - + +
131B VAL* 3.8 43.7 - - + +
132B LYS* 4.8 0.7 - - - -
133B ALA* 4.7 16.4 - - + -
901B C 5.5 1.8 - - - +
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Residues in contact with ASP 112 (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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108B ALA 5.0 0.6 + - - -
109B PRO 4.9 3.2 + - - +
110B HIS 3.5 0.2 - - - -
111B ILE* 1.3 81.5 - - - +
113B ALA* 1.3 57.9 + - - +
115B ARG* 3.4 29.6 + - - +
116B ALA* 2.9 29.5 + - - +
126B LEU* 5.2 7.1 - - - +
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Residues in contact with ALA 113 (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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25B VAL* 3.8 17.3 - - + -
109B PRO 5.5 0.6 + - - -
110B HIS* 3.4 13.9 + - + +
111B ILE 3.3 0.4 - - - -
112B ASP* 1.3 75.0 - - - +
114B MET* 1.3 54.6 + - - +
116B ALA* 3.1 7.7 + - - +
117B ASN* 2.8 42.9 + - - +
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Residues in contact with MET 114 (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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22B ILE* 3.5 42.4 - - + +
23B GLY* 3.5 15.7 - - - +
25B VAL* 3.8 5.1 - - + +
27B ILE* 4.0 18.4 - - + -
42B LEU* 3.9 14.4 - - + -
100B ILE* 3.7 26.0 - - + -
107B LEU* 4.5 11.9 - - + +
110B HIS* 3.1 23.9 + - + +
111B ILE* 3.5 11.7 - - - +
113B ALA* 1.3 76.5 - - - +
115B ARG* 1.3 56.9 - - - +
117B ASN* 3.1 3.3 + - - +
118B ILE* 2.9 35.7 + - + +
131B VAL* 4.3 8.3 - - + -
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Residues in contact with ARG 115 (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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55A ALA 4.4 14.7 + - - -
61A ARG* 5.5 6.5 - - - +
111B ILE* 2.9 36.9 + - - +
112B ASP* 3.4 27.7 + - - +
114B MET* 1.3 71.6 - - - +
116B ALA* 1.3 57.8 + - - +
118B ILE* 3.8 1.9 - - - +
119B ALA* 2.9 32.7 + - - +
126B LEU* 2.9 49.6 + - + +
127B ASP* 4.1 6.5 - - - +
129B VAL* 2.9 33.5 + - + +
130B ASN* 4.4 4.8 + - - +
131B VAL* 4.0 24.5 - - + +
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Residues in contact with ALA 116 (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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112B ASP 2.9 18.3 + - - +
113B ALA* 3.5 7.2 - - - +
115B ARG* 1.3 73.4 - - - +
117B ASN* 1.3 67.6 + - - +
119B ALA* 4.1 0.7 - - - +
120B ALA* 3.0 26.3 + - - +
126B LEU* 3.9 17.4 - - + +
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Residues in contact with ASN 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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23B GLY 3.0 24.8 + - - +
24B GLY* 3.6 20.8 + - - -
25B VAL* 3.7 8.1 - - - +
43B LEU* 6.0 0.9 - - + -
76B ARG* 3.4 34.4 + - + +
113B ALA* 2.8 22.8 + - - +
114B MET 3.4 6.5 - - - +
116B ALA* 1.3 74.8 - - - +
118B ILE* 1.3 62.1 + - + +
120B ALA* 3.5 1.8 + - - +
121B ASP* 3.0 32.0 + - - +
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Residues in contact with ILE 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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23B GLY* 5.1 0.2 - - - -
42B LEU* 3.8 13.9 - - + -
43B LEU* 3.7 22.9 - - + -
46B ILE* 3.7 29.8 - - + -
79B LEU* 4.4 10.8 - - + -
96B VAL* 5.0 1.3 - - + -
114B MET* 2.9 23.2 + - + +
117B ASN* 1.3 77.0 - - + +
119B ALA* 1.3 57.7 + - - +
121B ASP* 3.3 2.1 + - - +
122B LEU* 3.0 50.5 + - + +
129B VAL* 3.8 19.7 - - + -
131B VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 119 (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 ARG 2.9 22.6 + - - +
116B ALA 4.1 1.1 - - - +
118B ILE* 1.3 73.9 - - - +
120B ALA* 1.3 57.7 + - - +
122B LEU 3.4 0.3 + - - -
123B ASP* 2.9 9.7 + - - -
124B LEU* 2.9 47.7 + - - +
126B LEU* 4.1 20.4 - - + +
129B VAL* 3.9 19.9 - - + +
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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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76B ARG* 4.4 10.5 - - - +
116B ALA 3.0 18.8 + - - +
117B ASN* 3.6 5.2 - - - +
119B ALA* 1.3 75.2 - - - +
121B ASP* 1.3 62.5 + - - +
123B ASP* 3.1 15.1 + - - +
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Residues in contact with ASP 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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43B LEU* 5.0 0.7 - - - +
76B ARG* 2.7 55.1 + - - +
79B LEU* 3.7 25.2 - - + +
80B ARG* 2.9 51.6 + - + +
83B ALA* 4.1 7.1 - - - +
117B ASN* 3.0 20.2 + - - +
118B ILE 3.8 0.4 - - - +
120B ALA* 1.3 75.3 - - - +
122B LEU* 1.3 59.2 + - - +
123B ASP* 3.7 0.5 + - - +
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Residues in contact with LEU 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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46B ILE* 4.4 2.9 - - + -
50B LEU* 3.6 28.3 - - + -
79B LEU* 3.9 17.9 - - + -
83B ALA* 3.8 24.1 - - + +
93B ILE* 3.9 14.9 - - + +
96B VAL* 3.8 26.2 - - + -
118B ILE* 3.0 38.7 + - + +
119B ALA 4.3 0.4 - - - +
121B ASP* 1.3 76.2 - - - +
123B ASP* 1.3 71.4 + - - +
124B LEU* 3.3 27.5 + - + +
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Residues in contact with ASP 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 ALA 2.9 6.9 + - - -
120B ALA* 3.1 11.7 + - - +
121B ASP 3.4 1.3 - - - +
122B LEU* 1.3 79.9 - - - +
124B LEU* 1.3 61.5 + - - +
125B PRO* 4.3 2.8 - - - +
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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