Contacts of the helix formed by residues 98 - 115 (chain C) in PDB entry 2CUK
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 LEU 98 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C SER* 4.6 0.9 - - - -
74C VAL* 3.9 38.4 - - + +
94C THR 3.4 24.2 - - - +
96C GLY 3.1 7.4 - - - +
97C VAL* 1.3 77.9 - - + +
99C THR* 1.3 70.0 + - - +
100C GLU 3.5 1.8 - - - -
101C ALA* 3.5 3.2 + - - +
102C THR* 2.8 33.7 + - - +
155C ILE* 4.4 11.4 - - + -
280C SER* 3.9 15.3 - - - +
285C THR* 3.7 20.2 - - + -
289C MET* 3.9 26.7 - - + -
1401C NHE 5.4 0.9 - - - +
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Residues in contact with THR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLY* 3.2 31.3 + - - -
97C VAL 3.5 0.2 - - - -
98C LEU* 1.3 80.1 - - - +
100C GLU* 1.3 74.1 + - - +
102C THR* 3.4 2.1 + - - -
103C ALA* 3.0 21.7 + - - +
154C ARG* 3.5 47.8 + - + +
155C ILE* 3.9 15.4 - - - +
158C ALA* 3.8 11.9 - - + -
1401C NHE 4.9 0.9 + - - -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLN* 3.6 33.1 - - + +
166A PHE 5.0 0.9 - - - +
167A GLY* 5.9 0.3 - - - -
96C GLY 4.7 0.8 + - - -
97C VAL 5.2 1.7 + - - +
98C LEU 3.5 0.4 - - - -
99C THR* 1.3 90.2 - - - +
101C ALA* 1.3 59.3 + - - +
103C ALA* 3.3 1.9 + - - -
104C ASP* 2.9 36.0 + - - +
158C ALA* 4.0 7.6 - - - +
161C LYS* 4.5 10.2 + - - -
162C ARG* 2.6 35.5 + - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 2.9 28.9 + - - +
141A ASP* 3.5 12.8 + - - +
143A GLN* 4.6 1.0 + - - -
97C VAL 5.5 0.2 + - - -
98C LEU 3.5 7.9 + - - +
99C THR 3.3 0.4 - - - -
100C GLU* 1.3 77.8 - - - +
102C THR* 1.3 63.1 + - - +
104C ASP* 3.3 5.1 + - - -
105C LEU 3.1 9.9 + - - -
279C GLY 3.1 11.2 - - - +
280C SER* 4.1 6.3 - - - +
282C GLY 4.6 0.4 - - - +
285C THR* 3.4 33.9 + - + +
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Residues in contact with THR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 2.8 23.0 + - - +
99C THR 3.9 2.9 - - - -
101C ALA* 1.3 72.3 - - - +
103C ALA* 1.3 65.0 + - - +
105C LEU* 3.4 2.4 + - - +
106C THR* 2.8 28.1 + - - -
155C ILE* 4.0 31.4 - - + +
228C THR* 4.2 25.8 - - - +
279C GLY* 3.4 23.7 + - - -
280C SER* 4.1 7.4 + - - -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C THR 3.0 18.3 + - - +
100C GLU 3.7 4.5 - - - +
102C THR* 1.3 75.8 - - - +
104C ASP* 1.3 63.5 + - - +
106C THR* 3.3 1.7 + - - -
107C LEU* 3.1 29.3 + - - +
155C ILE* 4.4 2.6 - - - +
158C ALA* 3.6 26.2 - - + -
159C VAL* 3.8 22.2 - - + +
162C ARG* 3.8 15.7 - - - +
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Residues in contact with ASP 104 (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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111A LEU* 3.9 14.7 - - + +
115A ARG* 4.0 12.4 + - + +
140A LEU 5.6 0.2 - - - +
141A ASP* 5.1 1.2 - - - -
142A LEU* 4.1 14.3 + - + +
143A GLN* 3.0 25.4 + - - +
166A PHE* 3.0 17.7 - - - -
100C GLU 2.9 19.3 + - - +
101C ALA* 3.4 10.3 - - - +
102C THR 3.2 0.2 - - - -
103C ALA* 1.3 76.8 - - - +
105C LEU* 1.3 57.7 + - - +
107C LEU* 3.3 4.3 + - - +
108C ALA* 2.9 27.4 + - - +
162C ARG* 2.7 38.8 + - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.1 14.7 - - + +
117A VAL* 4.2 24.9 - - + -
101C ALA 3.1 13.5 + - - +
102C THR 3.8 3.8 - - - +
104C ASP* 1.3 75.3 - - - +
106C THR* 1.3 67.6 + - - +
108C ALA* 3.1 5.5 + - + +
109C LEU* 2.9 46.7 + - + +
228C THR* 4.1 5.4 - - + -
253C ASP* 3.7 22.2 - - + +
275C THR* 4.9 2.2 - - + +
278C ILE* 4.1 19.7 - - + +
279C GLY* 3.7 25.4 - - - +
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Residues in contact with THR 106 (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 THR* 2.8 20.2 + - - +
103C ALA 3.4 8.3 - - - -
104C ASP 3.2 0.2 - - - -
105C LEU* 1.3 78.6 - - - +
107C LEU* 1.3 61.7 + - + +
109C LEU* 3.3 4.2 + - - +
110C LEU* 3.1 21.0 + - - +
159C VAL* 4.0 18.3 - - + +
198C SER* 3.6 23.6 - - - +
200C HIS* 3.9 12.0 - - + -
226C LEU* 4.0 14.3 - - + +
228C THR* 3.1 33.2 + - + +
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Residues in contact with LEU 107 (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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111A LEU* 4.1 4.0 - - + -
166A PHE* 3.8 17.9 - - + -
103C ALA 3.1 18.3 + - - +
104C ASP 3.7 7.2 - - - +
106C THR* 1.3 74.3 - - + +
108C ALA* 1.3 66.1 + - - +
110C LEU* 3.2 22.2 + - + +
111C LEU* 3.0 31.1 + - + +
142C LEU* 5.7 1.1 - - + -
147C LEU* 6.1 0.2 - - + -
159C VAL* 3.8 28.9 - - + +
162C ARG* 3.7 29.6 - - + -
163C ALA* 4.5 9.0 - - + +
166C PHE* 4.0 28.7 - - + -
168C MET* 5.9 0.2 - - - -
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Residues in contact with ALA 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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108A ALA 5.7 1.5 - - - +
111A LEU* 3.7 32.3 - - + +
112A ALA 5.2 0.2 - - - +
115A ARG* 5.4 1.3 - - + -
117A VAL* 3.8 25.0 - - + +
104C ASP 2.9 14.5 + - - +
105C LEU* 3.3 13.0 - - + +
107C LEU* 1.3 77.7 - - - +
109C LEU* 1.3 57.1 + - - +
111C LEU* 3.4 3.6 + - - +
112C ALA* 2.8 30.6 + - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 4.5 6.3 - - + -
105C LEU* 2.9 40.3 + - + +
106C THR 3.6 4.7 - - - +
108C ALA* 1.3 75.4 - - - +
110C LEU* 1.3 59.6 + - - +
112C ALA* 3.5 1.3 - - - +
113C VAL* 2.9 36.7 + - - +
226C LEU* 4.4 5.2 - - + -
228C THR* 4.0 10.3 - - + -
251C GLY* 4.0 13.7 - - - +
252C LEU 3.9 3.1 - - - -
253C ASP* 3.9 25.1 - - + +
273C VAL* 3.9 34.3 - - + +
275C THR* 3.9 21.5 - - + +
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Residues in contact with LEU 110 (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 THR 3.1 14.2 + - - +
107C LEU* 3.2 23.8 + - + +
109C LEU* 1.3 75.8 - - - +
111C LEU* 1.3 57.9 + - - +
113C VAL* 3.8 0.8 - - - +
114C ALA* 2.8 33.4 + - - +
142C LEU* 4.0 32.3 - - + -
147C LEU* 5.3 5.4 - - + -
168C MET* 4.0 19.3 - - - -
196C VAL* 3.9 34.3 - - + -
224C ILE* 4.2 15.3 - - + -
226C LEU* 3.8 21.4 - - + +
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Residues in contact with LEU 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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104A ASP* 3.8 21.3 - - + +
107A LEU 4.1 0.2 - - - -
108A ALA* 3.6 37.0 - - + +
111A LEU* 4.0 13.0 - - + -
107C LEU* 3.0 23.0 + - + +
108C ALA 3.8 3.1 - - - +
110C LEU* 1.3 73.8 - - + +
112C ALA* 1.3 62.2 + - - +
114C ALA* 4.5 2.5 - - - -
115C ARG* 2.9 39.9 + - + +
117C VAL* 3.9 3.8 - - - +
142C LEU* 3.7 27.4 - - + -
166C PHE* 3.9 32.5 - - + -
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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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108A ALA* 5.0 0.6 - - - +
117A VAL* 4.5 9.2 - - + -
108C ALA 2.8 19.7 + - - +
109C LEU* 3.2 9.2 + - - +
111C LEU* 1.3 76.8 - - - +
113C VAL* 1.3 56.1 + - - +
116C ARG* 3.1 8.5 + - - -
117C VAL* 3.1 36.0 + - + -
118C VAL* 4.3 21.1 + - + -
273C VAL* 4.4 16.2 - - + +
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Residues in contact with VAL 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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109C LEU 2.9 20.5 + - - +
110C LEU* 3.9 2.5 - - - +
112C ALA* 1.3 75.9 - - - +
114C ALA* 1.3 67.3 + - - +
116C ARG* 3.1 16.3 + - - +
224C ILE* 3.9 19.7 - - + -
226C LEU* 5.2 0.2 - - + -
248C PHE* 3.6 12.6 - - + -
249C GLY* 3.9 9.6 - - - -
250C ALA 3.5 45.8 - - - +
251C GLY* 3.7 8.5 - - - +
271C ASN* 3.9 10.5 - - - +
273C VAL* 3.8 17.7 - - + -
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Residues in contact with ALA 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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110C LEU 2.8 23.7 + - - +
111C LEU* 4.3 3.1 - - - +
113C VAL* 1.3 74.9 - - - +
115C ARG* 1.3 61.7 + - + +
139C GLY* 3.2 6.8 - - - -
140C LEU* 2.8 43.3 + - + +
142C LEU* 4.0 21.1 - - + -
224C ILE* 3.9 18.8 - - + +
248C PHE* 3.9 6.5 - - - -
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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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101A ALA* 2.8 34.3 + - - +
104A ASP* 3.8 11.1 + - + +
105A LEU* 4.0 17.0 - - + +
108A ALA* 5.3 0.2 - - + -
278A ILE* 2.9 42.3 + - - +
279A GLY* 3.0 12.5 + - - -
280A SER 3.8 0.2 - - - -
281A ALA* 3.1 30.8 + - - +
282A GLY* 3.7 5.3 - - - +
111C LEU* 2.9 32.8 + - + +
112C ALA 4.0 0.2 - - - -
114C ALA* 1.3 79.4 - - + +
116C ARG* 1.3 73.8 + - - +
117C VAL* 3.2 12.0 + - + -
137C LEU 4.8 4.1 - - - +
139C GLY* 4.7 2.7 - - - -
140C LEU 3.7 23.8 - - - +
141C ASP* 4.8 3.0 + - - +
142C LEU* 6.2 1.3 - - + -
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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
------------------------------------------------------------
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