Contacts of the helix formed by residues 107 - 118 (chain C) in PDB entry 3DH1
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 CYS 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B LEU* 5.2 0.2 - - - -
71C HIS* 3.6 14.1 - - + -
105C GLU 3.6 2.4 + - - -
106C PRO* 1.3 74.9 - - - +
108C ILE* 1.3 61.9 + - - +
109C MET* 3.1 12.8 - - - -
110C CYS* 3.4 14.8 - - - -
111C ALA* 2.8 28.8 + - - +
128C ASN* 3.7 11.6 - - - +
131C PHE* 3.0 31.6 - - + +
133C GLY 3.6 1.3 - - - -
201C ZN 2.4 37.7 - - - -
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Residues in contact with ILE 108 (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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108B ILE* 3.7 25.6 - - + -
112B ALA* 4.2 8.1 - - + -
140B ILE* 3.7 27.1 - - + -
145B LEU* 5.1 1.6 - - + -
107C CYS* 1.3 73.4 - - - +
109C MET* 1.3 57.4 + - - +
111C ALA* 3.9 1.6 - - - +
112C ALA* 3.1 26.3 + - - +
131C PHE* 2.8 46.7 + - + +
132C GLY 3.9 9.4 - - - +
133C GLY* 4.0 10.1 - - - -
137C VAL* 4.3 15.5 - - + -
138C LEU* 3.8 21.3 - - + -
140C ILE* 4.3 8.2 - - + +
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Residues in contact with MET 109 (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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74B MET* 4.7 4.3 - - + -
109B MET* 3.6 33.6 - - + +
112B ALA* 3.7 18.5 - - + +
113B ALA* 4.2 8.5 - - + +
116B LEU* 3.8 25.4 - - + -
69C THR* 3.6 46.7 - - + +
71C HIS* 5.3 1.6 - - - -
74C MET* 3.8 28.0 - - + -
107C CYS* 3.1 12.4 - - - -
108C ILE* 1.3 77.9 - - - +
110C CYS* 1.3 66.6 + - - +
112C ALA* 3.3 4.0 + - - -
113C ALA* 3.1 18.7 + - - +
131C PHE* 4.5 0.6 - - + -
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Residues in contact with CYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C HIS* 3.6 15.3 - - - -
73C GLU* 3.5 36.1 - - + +
74C MET* 4.1 13.5 - - - -
106C PRO* 4.0 7.4 - - + -
107C CYS* 3.4 4.1 + - - -
109C MET* 1.3 80.0 - - - +
111C ALA* 1.3 66.1 + - - +
113C ALA* 3.0 18.8 + - - +
114C LEU* 3.0 18.5 + - + +
201C ZN 2.4 34.8 - - - -
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Residues in contact with ALA 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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106C PRO* 3.8 13.1 - - + +
107C CYS 2.8 23.3 + - - +
108C ILE 3.9 2.9 - - - +
110C CYS* 1.3 72.9 - - - +
112C ALA* 1.3 59.1 + - - +
114C LEU* 3.5 2.1 + - - -
115C ARG 3.4 15.8 + - - -
133C GLY* 3.6 29.8 - - - +
134C CYS* 4.7 0.4 - - - -
140C ILE* 3.7 14.0 - - + +
152C PHE* 3.6 24.1 - - + -
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Residues in contact with ALA 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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108B ILE* 4.0 10.3 - - + -
109B MET* 3.8 16.6 - - + -
131B PHE* 3.7 25.3 - - + -
108C ILE 3.1 19.5 + - - +
109C MET 3.7 4.5 - - - +
110C CYS 3.1 0.6 - - - -
111C ALA* 1.3 72.9 - - - +
113C ALA* 1.3 65.2 + - - +
115C ARG* 3.5 4.5 + - - +
116C LEU* 3.2 28.4 + - - +
140C ILE* 3.9 9.8 - - + +
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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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69B THR* 4.1 19.3 - - + -
109B MET* 4.1 14.7 - - - +
74C MET* 4.2 19.1 - - - -
77C ILE* 4.5 7.6 - - + -
109C MET 3.1 11.8 + - - +
110C CYS* 3.0 10.5 + - - +
112C ALA* 1.3 74.5 - - - +
114C LEU* 1.3 59.7 + - + +
116C LEU* 2.8 23.0 + - - +
117C MET* 2.9 17.5 + - - +
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Residues in contact with LEU 114 (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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48C MET* 5.4 1.6 - - + -
73C GLU* 5.3 8.1 - - + -
77C ILE* 4.1 20.0 - - + -
100C LEU* 3.6 31.2 - - + -
106C PRO* 4.4 14.4 - - + -
110C CYS* 3.0 22.1 + - + +
111C ALA 3.9 0.2 - - - +
112C ALA 3.3 0.2 - - - -
113C ALA* 1.3 76.6 - - + +
115C ARG* 1.3 56.5 + - - +
117C MET* 3.4 4.3 + - - -
118C LYS* 2.8 23.6 + - - -
119C ILE* 3.4 36.5 + - + +
122C VAL* 4.0 17.5 - - + -
152C PHE* 3.9 22.9 - - + -
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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
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131B PHE* 5.2 5.8 - - + -
111C ALA 3.4 9.2 + - - +
112C ALA* 3.6 9.4 - - - +
113C ALA 3.2 0.4 - - - -
114C LEU* 1.3 75.5 - - - +
116C LEU* 1.3 66.9 + - + +
118C LYS* 3.2 9.1 + - - +
140C ILE* 2.9 42.4 + - - +
143C ALA* 2.9 32.5 + - - +
145C LEU* 3.5 40.8 + - - +
148C THR 3.4 18.5 + - - +
149C GLY* 3.1 20.3 + - - -
150C ARG 3.3 20.0 + - - +
151C PRO* 3.5 35.6 - - - +
152C PHE* 4.1 11.8 - - + -
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Residues in contact with LEU 116 (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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68B ALA* 3.1 33.4 - - + +
69B THR* 5.1 0.4 - - - +
71B HIS* 4.1 27.4 - - + +
109B MET* 3.7 27.6 - - + -
131B PHE* 4.3 25.8 - - + -
112C ALA 3.2 14.6 + - - +
113C ALA* 2.8 10.3 + - - +
115C ARG* 1.3 78.5 - - + +
117C MET* 1.3 59.5 + - - +
118C LYS* 3.9 10.7 - - - +
148C THR* 4.7 7.4 - - + +
149C GLY* 4.3 17.6 - - - +
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Residues in contact with MET 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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66B LYS 5.3 1.3 - - - +
67B ASN* 4.0 7.2 - - - +
68B ALA* 3.6 30.3 - - - +
69B THR* 3.8 15.3 - - + -
77C ILE* 3.5 31.2 - - + -
81C LEU* 4.4 7.4 - - + -
91C PRO* 5.6 0.2 - - + -
92C SER* 5.7 1.7 - - - -
95C PHE* 3.3 61.5 - - + +
96C GLU* 4.4 2.1 + - - +
113C ALA 2.9 18.4 + - - +
114C LEU 3.8 0.4 - - - +
116C LEU* 1.3 76.8 - - - +
118C LYS* 1.3 69.2 + - - +
119C ILE* 3.4 21.8 + - + -
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Residues in contact with LYS 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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95C PHE 4.2 1.3 - - - -
96C GLU* 3.6 36.7 + - + +
114C LEU 2.8 8.9 + - - -
115C ARG* 3.2 15.3 + - - +
116C LEU 3.9 7.2 - - - +
117C MET* 1.3 81.0 - - - +
119C ILE* 1.3 67.9 + - - +
120C PRO* 3.2 9.5 - - - +
149C GLY* 4.4 17.2 - - - +
150C ARG* 3.6 54.6 - - + +
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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