Contacts of the helix formed by residues 95 - 104 (chain C) in PDB entry 2CX9
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 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C SER* 2.8 36.4 + - - +
94C SER* 1.3 76.4 - - - +
96C ALA* 1.3 68.8 + - - +
99C HIS* 2.9 28.8 + - - +
125C TRP* 3.4 50.9 - - + +
160C THR* 5.7 3.8 - - - +
244C VAL* 3.8 22.8 - - + +
245C LEU* 4.5 4.9 - - + -
369C GLU* 4.0 35.2 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C SER 3.7 2.6 + - - +
92C HIS 3.8 6.5 - - - +
95C LEU* 1.3 81.5 - - - +
97C THR* 1.3 67.4 + - - +
99C HIS* 3.4 2.4 + - - +
100C ILE* 3.4 24.7 + - + +
116C LEU* 5.2 2.2 - - + -
123C GLY* 3.5 40.6 - - - +
124C ALA 3.7 9.9 - - - +
125C TRP* 3.9 5.0 - - - +
167C VAL* 5.0 1.3 - - + +
169C VAL* 3.9 16.2 - - + +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE 5.2 4.3 - - - +
56C LEU* 6.6 0.4 - - + -
57C VAL* 3.5 31.6 - - + -
92C HIS* 3.1 27.3 + - - -
93C ASN* 3.4 11.9 - - - +
96C ALA* 1.3 75.8 - - - +
98C GLY* 1.3 66.6 - - - +
100C ILE* 3.0 5.4 + - - +
101C LEU* 2.9 23.2 + - + +
113C LEU* 3.9 10.3 - - + -
116C LEU* 3.5 33.0 - - + +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 6.5 0.9 - - - -
93C ASN 2.7 21.7 + - - -
94C SER* 3.6 11.4 - - - -
95C LEU 3.4 0.8 + - - -
96C ALA 3.4 0.8 - - - -
97C THR* 1.3 74.8 - - - +
99C HIS* 1.3 55.9 + - - +
101C LEU* 3.4 9.1 + - - +
102C LEU* 2.9 32.2 + - - +
244C VAL* 4.6 2.9 - - - -
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C LEU 2.9 21.7 + - - +
96C ALA 3.8 3.4 - - - +
98C GLY* 1.3 72.7 - - - +
100C ILE* 1.3 58.5 + - - +
102C LEU* 3.3 0.8 + - + -
103C ALA* 2.8 35.3 + - + +
125C TRP* 3.1 23.1 + - + +
169C VAL* 3.8 4.0 - - + +
171C MET* 3.7 14.7 - - - +
189C ALA* 3.5 28.7 - - + +
231C LEU* 3.4 23.0 + - + +
237C GLY 4.4 1.3 + - - -
240C ASP* 3.8 18.7 + - + +
241C VAL* 4.3 15.5 - - + -
244C VAL* 3.7 21.9 - - + +
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Residues in contact with ILE 100 (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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96C ALA 3.4 10.1 + - - +
97C THR 3.0 7.9 + - - +
99C HIS* 1.3 74.1 - - - +
101C LEU* 1.3 60.5 + - - +
104C GLY* 2.7 35.4 + - - +
108C GLN* 4.4 4.7 - - + +
109C LYS* 4.1 14.4 - - - +
112C PHE* 3.7 27.8 - - + -
113C LEU* 3.7 21.3 - - + -
116C LEU* 3.5 26.9 - - + -
167C VAL* 4.1 13.0 - - + -
169C VAL* 4.1 15.7 - - + -
191C ALA* 4.3 11.0 - - + -
231C LEU* 4.1 9.6 - - + -
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Residues in contact with LEU 101 (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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56C LEU* 3.7 29.4 - - + +
57C VAL* 4.0 9.9 - - + -
58C PRO* 3.9 23.6 - - + -
61C TYR* 5.3 2.2 - - + -
97C THR* 2.9 16.2 + - + +
98C GLY* 3.8 7.6 - - - +
100C ILE* 1.3 77.5 - - - +
102C LEU* 1.3 60.3 + - - +
109C LYS* 3.8 23.9 + - + +
113C LEU* 3.8 28.7 - - + -
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Residues in contact with LEU 102 (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 GLY 2.9 17.7 + - - +
99C HIS* 3.6 3.1 - - - +
100C ILE 3.1 0.2 - - - -
101C LEU* 1.3 81.1 - - - +
103C ALA* 1.3 61.4 + - + +
104C GLY 3.6 0.8 - - - +
109C LYS* 5.7 0.5 - - - -
240C ASP* 3.8 14.8 - - + +
243C ARG* 3.6 67.1 + - + +
244C VAL* 3.9 13.7 - - + +
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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
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99C HIS* 2.8 18.5 + - + +
102C LEU* 1.3 74.1 - - - +
104C GLY* 1.3 64.6 + - - +
105C SER 3.7 1.0 + - - -
108C GLN* 3.9 0.7 - - - +
231C LEU* 3.6 21.3 - - + +
232C GLY* 3.8 18.3 + - - -
240C ASP* 3.6 31.2 - - + +
243C ARG* 5.1 1.3 - - - +
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Residues in contact with GLY 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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100C ILE* 2.7 26.7 + - - -
101C LEU 4.5 0.2 - - - -
102C LEU 3.6 1.2 - - - +
103C ALA* 1.3 74.4 - - - +
105C SER* 1.3 65.2 + - - -
108C GLN* 3.2 15.0 - - - -
109C LYS* 2.9 27.6 + - - -
231C LEU* 3.4 8.2 - - - +
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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
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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