Contacts of the helix formed by residues 124 - 139 (chain C) in PDB entry 3U1K
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 SER 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C GLN* 3.7 10.8 + - - -
122C GLY 4.2 1.0 + - - -
123C THR* 1.3 73.2 - - - +
125C ASP* 1.3 66.2 + - - +
126C LYS* 3.6 4.1 + - - +
127C GLU* 2.8 37.4 + - - +
128C ILE* 3.1 25.6 + - - +
415C ILE* 3.6 37.5 - - - +
416C ASN* 3.7 10.1 - - - +
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Residues in contact with ASP 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C THR 4.9 1.2 - - - +
124C SER* 1.3 74.6 - - - +
126C LYS* 1.3 58.4 + - - +
128C ILE* 3.3 1.3 + - - +
129C LEU* 2.8 41.3 + - + +
416C ASN* 3.2 27.7 + - - +
419C LYS* 5.1 11.4 + - - +
448C LEU* 3.1 40.0 - - + +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 4.6 11.9 - - + -
104C GLN* 4.0 22.7 - - - +
124C SER* 3.2 9.2 + - - +
125C ASP* 1.3 79.8 - - - +
127C GLU* 1.3 58.2 + - - +
129C LEU* 3.8 7.9 - - + +
130C THR* 2.8 48.0 + - - +
164C GLU* 4.1 13.3 + - - -
165C PRO* 5.9 2.2 - - - -
166C ASP* 2.9 35.5 + - - +
192C ARG* 5.1 0.2 - - - +
415C ILE 5.8 2.0 - - - +
416C ASN* 4.7 0.6 + - - -
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Residues in contact with GLU 127 (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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102C TYR* 3.4 27.4 - - + +
103C ARG* 3.3 8.5 - - - +
104C GLN* 2.8 50.5 + - + +
122C GLY 4.7 1.4 - - - +
123C THR* 3.2 22.8 - - + +
124C SER* 2.8 41.4 + - - +
126C LYS* 1.3 75.3 - - - +
128C ILE* 1.3 63.1 + - + +
130C THR* 4.0 0.7 - - - -
131C SER* 2.8 31.6 + - - -
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C THR* 3.6 34.3 - - + +
124C SER 3.1 25.4 + - - +
125C ASP 3.8 5.2 - - - +
127C GLU* 1.3 77.5 - - - +
129C LEU* 1.3 66.7 + - + +
131C SER* 3.4 5.9 + - - -
132C ARG* 3.0 40.9 + - + +
443C LEU* 4.4 10.8 - - + -
445C ARG* 3.9 41.5 - - + +
448C LEU* 4.0 30.5 - - + -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ASP* 2.8 30.6 + - + +
126C LYS* 3.9 7.2 - - + +
128C ILE* 1.3 78.9 - - + +
130C THR* 1.3 58.3 + - - +
132C ARG* 3.3 8.5 + - + +
133C ILE* 3.0 37.8 + - + +
448C LEU* 3.8 21.5 - - + -
449C GLY* 3.9 15.5 - - - -
452C ALA* 3.8 28.5 - - + -
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.5 36.5 - - + -
126C LYS* 2.8 44.4 + - - +
129C LEU* 1.3 74.5 - - - +
131C SER* 1.3 65.6 + - - +
133C ILE* 3.1 12.1 + - + +
134C ILE* 2.9 32.4 + - + +
166C ASP* 3.7 25.5 + - + +
170C ILE* 5.7 0.9 - - + -
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Residues in contact with SER 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 3.4 33.3 + - - +
101C ASP* 3.9 1.0 + - - -
102C TYR* 3.0 26.6 + - - +
127C GLU 2.8 21.8 + - - -
128C ILE* 3.4 8.1 - - - -
130C THR* 1.3 75.6 - - - +
132C ARG* 1.3 58.3 + - - +
134C ILE* 3.3 2.3 + - - +
135C ASP* 2.8 29.7 + - - +
445C ARG* 6.0 4.9 - - - -
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Residues in contact with ARG 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C CIT 2.5 55.7 + - - -
128C ILE* 3.0 28.6 + - + +
129C LEU* 3.6 8.7 - - + +
130C THR 3.1 0.2 - - - -
131C SER* 1.3 79.0 - - - +
133C ILE* 1.3 64.9 + - - +
135C ASP* 3.3 8.5 + - + +
136C ARG* 3.0 51.7 + - - +
445C ARG* 3.7 25.7 + - + +
446C ARG* 3.5 28.7 - - - +
449C GLY* 4.0 12.7 - - - -
450C HIS* 4.2 6.7 - - - -
558C GLN* 4.9 1.4 + - - -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.0 22.6 + - + +
130C THR* 3.1 11.9 + - + +
132C ARG* 1.3 73.7 - - - +
134C ILE* 1.3 64.8 + - - +
136C ARG* 3.4 23.0 + - - +
137C SER* 2.9 27.2 + - - -
166C ASP* 5.9 4.9 - - + +
170C ILE* 3.7 25.4 - - + -
192C ARG* 6.0 1.6 - - - +
217C VAL* 4.5 11.4 - - + -
228C MET* 3.7 22.1 - - + +
230C GLU* 3.9 22.0 - - + -
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Residues in contact with ILE 134 (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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100C VAL* 3.6 19.3 - - + -
102C TYR* 4.0 6.5 - - + -
130C THR* 2.9 31.1 + - + +
131C SER 3.6 4.0 - - - +
133C ILE* 1.3 77.0 - - - +
135C ASP* 1.3 63.8 + - - +
137C SER* 3.0 18.3 + - - -
138C ILE* 3.3 13.3 + - + +
152C VAL* 4.8 0.9 - - + -
154C CYS* 3.8 17.0 - - - -
169C ALA* 3.6 27.6 - - + -
170C ILE* 3.6 25.6 - - + -
173C ALA* 3.8 29.4 - - + -
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Residues in contact with ASP 135 (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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98C LEU* 4.0 10.8 - - - +
99C VAL* 5.0 0.2 - - - -
100C VAL* 3.7 21.3 + - + +
131C SER 2.8 18.1 + - - +
132C ARG* 3.5 10.3 - - + +
134C ILE* 1.3 76.2 - - - +
136C ARG* 1.3 64.1 + - - +
138C ILE* 3.1 3.9 + - - +
139C ARG* 2.8 76.2 + - - +
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Residues in contact with ARG 136 (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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1C CIT 4.2 7.1 + - - +
132C ARG* 3.0 51.4 + - - +
133C ILE* 3.9 19.9 - - - +
135C ASP* 1.3 83.4 - - + +
137C SER* 1.3 59.2 + - - +
139C ARG* 4.8 3.6 - - - +
140C PRO* 3.4 20.7 - - - +
227C VAL* 3.9 6.8 - - - +
228C MET* 3.8 22.7 - - + +
230C GLU* 3.0 29.9 + - - +
558C GLN* 3.5 22.3 + - - +
559C ALA 4.7 2.7 + - - +
560C ASP* 2.6 44.0 + - + +
561C ILE 4.9 1.9 + - - +
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Residues in contact with SER 137 (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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133C ILE 2.9 16.7 + - - -
134C ILE 3.0 11.5 + - - -
136C ARG* 1.3 76.9 - - - +
138C ILE* 1.3 62.0 + - - +
141C LEU* 4.6 0.2 - - - +
170C ILE* 3.7 25.9 - - - +
188C VAL* 3.6 19.9 - - - +
219C ALA* 3.6 19.9 - - - +
227C VAL* 3.5 17.7 - - - +
228C MET* 3.6 18.4 - - - +
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Residues in contact with ILE 138 (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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98C LEU* 4.3 12.1 - - + -
100C VAL* 3.9 25.1 - - + -
134C ILE* 3.6 15.0 - - + +
135C ASP* 3.5 8.7 - - - +
137C SER* 1.3 86.6 - - - +
139C ARG* 1.3 70.3 + - - +
140C PRO* 3.3 3.4 - - - -
141C LEU* 3.2 7.0 + - - +
142C PHE* 3.5 4.0 - - + -
152C VAL* 4.0 21.1 - - + -
170C ILE* 5.1 2.7 - - + +
173C ALA* 4.1 18.6 - - + -
174C SER* 4.7 4.9 - - - +
177C LEU* 4.1 10.8 - - + -
184C TRP* 2.9 44.9 + - + +
188C VAL* 5.7 0.9 - - + -
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Residues in contact with ARG 139 (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* 6.0 1.0 - - - -
96C MET* 4.1 26.7 + - + +
98C LEU* 3.1 40.2 + - + +
135C ASP* 2.8 53.2 + - - +
136C ARG* 4.8 1.8 - - - +
138C ILE* 1.3 79.4 - - - +
140C PRO* 1.3 67.6 - - + +
141C LEU 3.1 1.6 + - - -
142C PHE* 3.4 25.2 + - + +
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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
------------------------------------------------------------
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