Contacts of the helix formed by residues 110 - 122 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.9 25.0 - - + +
26C THR 4.9 2.4 + - - -
27C ILE* 3.8 32.7 - - + +
28C PRO* 4.5 11.1 - - + +
106C LYS 3.7 14.9 + - - -
107C LEU* 2.8 9.1 + - - +
109C PRO* 1.3 104.4 - - + +
111C ILE* 1.3 64.3 + - - +
112C ASP 3.4 2.5 - - - -
113C ALA* 3.3 11.2 + - - +
114C MET* 3.1 38.7 + - + +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP* 4.5 5.6 - - - +
61B ARG* 4.0 24.7 - - - +
100C ILE* 5.0 0.9 - - + -
107C LEU* 3.5 24.0 - - + +
108C ALA* 3.6 12.4 + - - +
110C HIS* 1.3 74.2 - - - +
112C ASP* 1.3 67.9 + - - +
114C MET* 3.2 13.6 + - - +
115C ARG* 3.0 23.8 + - + +
131C VAL* 3.4 38.7 - - + +
132C LYS 4.8 0.7 - - - -
133C ALA* 4.0 19.5 - - + +
901C C 3.8 22.2 - - - +
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Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 3.7 30.7 + - - -
108C ALA 4.9 2.3 + - - +
109C PRO 5.2 2.9 + - - +
110C HIS 3.4 1.2 - - - -
111C ILE* 1.3 77.8 - - - +
113C ALA* 1.3 56.1 + - - +
115C ARG* 3.4 21.3 + - - +
116C ALA* 3.0 27.2 + - - +
126C LEU* 5.2 0.9 - - - +
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C VAL* 3.8 18.8 - - + -
109C PRO 5.5 1.3 + - - +
110C HIS* 3.3 13.1 + - - +
111C ILE 3.3 0.2 - - - -
112C ASP* 1.3 76.4 - - - +
114C MET* 1.3 55.4 + - - +
116C ALA* 3.2 8.0 + - - +
117C ASN* 2.8 41.1 + - - +
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Residues in contact with MET 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.5 38.6 - - + +
23C GLY* 3.5 15.0 - - - +
25C VAL* 3.6 5.1 - - + +
27C ILE* 3.9 21.5 - - + -
42C LEU* 3.9 8.1 - - + -
100C ILE* 3.5 29.2 - - + -
107C LEU* 4.6 9.6 - - + -
110C HIS* 3.1 27.4 + - + +
111C ILE* 3.3 11.7 - - - +
113C ALA* 1.3 74.6 - - - +
115C ARG* 1.3 57.0 + - - +
117C ASN* 3.2 4.0 + - - +
118C ILE* 2.9 35.8 + - - +
131C VAL* 4.2 12.8 - - + -
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 2.7 33.2 + - - +
56B LEU* 5.9 0.4 - - - +
57B GLY* 5.5 2.6 - - - +
61B ARG* 5.4 8.8 - - - +
111C ILE* 3.0 14.6 + - + +
112C ASP* 3.5 24.0 + - - +
114C MET* 1.3 75.5 - - - +
116C ALA* 1.3 55.0 + - - +
118C ILE 3.4 0.7 + - - -
119C ALA* 2.9 32.2 + - - +
126C LEU* 3.1 40.3 + - + +
127C ASP* 4.2 3.4 - - - +
129C VAL* 2.8 44.8 + - + +
130C ASN* 4.6 8.2 + - - +
131C VAL* 4.2 11.8 - - + +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP 3.0 14.1 + - - +
113C ALA* 3.2 11.9 + - - +
115C ARG* 1.3 76.6 - - - +
117C ASN* 1.3 64.8 + - - +
119C ALA* 3.5 1.6 + - - +
120C ALA* 3.0 25.0 + - - +
126C LEU* 3.7 19.7 - - + +
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Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY 3.0 22.8 + - - +
24C GLY* 3.5 21.0 + - - -
25C VAL* 3.7 8.1 - - - +
43C LEU* 6.1 0.7 - - + -
76C ARG* 3.2 41.4 + - - +
113C ALA* 2.8 22.0 + - - +
114C MET 3.3 8.5 - - - +
116C ALA* 1.3 75.0 - - - +
118C ILE* 1.3 57.7 + - + +
120C ALA* 3.3 2.1 + - - -
121C ASP* 3.0 28.3 + - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY* 4.8 0.9 - - - -
42C LEU* 4.0 13.2 - - + -
43C LEU* 3.7 23.1 - - + -
46C ILE* 3.6 32.5 - - + -
79C LEU* 4.5 9.9 - - + -
96C VAL* 4.9 2.0 - - + -
114C MET* 2.9 21.5 + - + +
115C ARG 3.9 2.9 - - - +
117C ASN* 1.3 71.7 - - + +
119C ALA* 1.3 61.2 + - - +
121C ASP* 3.2 1.8 + - - +
122C LEU* 2.9 52.1 + - + +
129C VAL* 3.8 16.6 - - + -
131C VAL* 3.7 25.1 - - + -
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ARG 2.9 18.3 + - - +
116C ALA 3.9 2.7 - - - +
118C ILE* 1.3 75.1 - - - +
120C ALA* 1.3 62.2 + - - +
122C LEU* 4.8 0.2 - - - -
123C ASP* 3.0 4.3 + - - -
124C LEU* 2.8 47.9 + - - +
125C PRO 4.3 5.4 - - - +
126C LEU* 4.3 15.5 - - + +
129C VAL* 3.9 21.5 - - + +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 4.2 10.1 - - - +
116C ALA 3.0 19.4 + - - +
117C ASN* 3.4 5.6 - - - +
118C ILE 3.2 0.2 - - - -
119C ALA* 1.3 76.6 - - - +
121C ASP* 1.3 63.3 + - - +
123C ASP* 3.2 13.8 + - - +
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU* 5.1 1.4 - - - +
76C ARG* 2.8 40.6 + - - +
79C LEU* 3.7 26.2 - - + +
80C ARG* 2.8 62.1 + - + +
83C ALA* 4.3 5.0 - - - +
117C ASN* 3.0 17.8 + - - +
118C ILE* 3.2 1.0 + - - +
120C ALA* 1.3 76.3 - - - +
122C LEU* 1.3 63.0 + - - +
123C ASP* 3.3 1.4 + - - +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 4.5 3.1 - - + -
50C LEU* 3.6 28.3 - - + -
79C LEU* 4.0 18.8 - - + -
83C ALA* 3.8 25.2 - - + +
93C ILE* 3.9 13.3 - - + +
96C VAL* 3.9 26.2 - - + -
118C ILE* 2.9 38.5 + - + +
119C ALA 4.3 0.7 - - - +
121C ASP* 1.3 75.3 - - - +
123C ASP* 1.3 70.6 + - - +
124C LEU* 3.2 27.8 + - + +
129C VAL* 5.1 0.7 - - + -
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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