Contacts of the helix formed by residues 94 - 108 (chain C) in PDB entry 2HNK
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 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C ASP* 2.9 14.9 + - - -
93C VAL* 1.3 78.9 - - - +
95C GLU* 1.3 54.9 + - - +
96C GLU* 3.5 7.3 + - - +
97C TRP* 3.0 47.6 + - - +
98C THR* 2.7 35.4 + - - +
118C LEU* 3.5 2.9 - - - +
2003C SAH 4.0 3.6 - - - -
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Residues in contact with GLU 95 (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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93C VAL 3.8 3.2 + - - -
94C SER* 1.3 70.2 - - - +
96C GLU* 1.3 60.9 + - - +
98C THR* 3.4 6.5 + - - -
99C ASN* 2.9 60.9 + - - +
118C LEU* 4.0 24.3 - - + +
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Residues in contact with GLU 96 (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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94C SER* 3.3 6.8 + - - +
95C GLU* 1.3 81.8 - - - +
97C TRP* 1.3 83.2 + - + +
99C ASN* 3.3 20.5 + - - +
100C VAL* 3.5 11.5 + - + +
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Residues in contact with TRP 97 (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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37C LEU* 4.4 13.3 - - + +
39C GLN* 3.3 41.5 + - + -
42C MET* 3.8 14.4 - - + -
70C PHE* 3.1 45.2 - + - +
71C THR* 3.6 10.0 - - + +
94C SER* 3.0 23.7 + - - +
96C GLU* 1.3 94.4 + - + +
98C THR* 1.3 62.2 + - + +
99C ASN 3.1 1.6 - - - -
100C VAL* 3.1 13.3 + - + +
101C ALA 3.1 20.3 + - - -
2003C SAH 3.3 39.3 - - - -
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Residues in contact with THR 98 (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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69C THR* 4.3 8.1 - - + -
70C PHE 4.0 7.9 - - - +
92C ASP* 3.5 31.6 - - + -
94C SER 2.7 22.9 + - - +
95C GLU* 3.4 6.2 + - - -
97C TRP* 1.3 73.2 - - - +
99C ASN* 1.3 61.6 + - - +
100C VAL 3.3 0.2 - - - -
101C ALA* 3.5 8.7 - - - +
102C ARG* 2.9 29.1 + - - +
105C TRP* 4.9 2.6 - - - -
116C LEU* 4.0 28.6 - - + +
118C LEU* 3.3 14.4 - - + +
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Residues in contact with ASN 99 (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 GLU* 2.9 54.7 + - - +
96C GLU* 3.3 11.2 - - - +
97C TRP 3.1 0.2 - - - -
98C THR* 1.3 75.5 + - - +
100C VAL* 1.3 63.3 + - - +
102C ARG* 4.2 7.2 - - - +
103C LYS* 3.2 20.6 + - - +
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Residues in contact with VAL 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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30C LEU* 4.0 3.8 - - + -
33C GLU* 3.5 30.1 - - + +
34C THR 6.1 0.2 - - - +
37C LEU* 5.5 4.3 - - + -
71C THR* 3.9 29.2 - - + -
96C GLU* 3.8 14.8 - - + +
97C TRP* 3.1 12.8 + - + +
99C ASN* 1.3 74.4 - - + +
101C ALA* 1.3 66.3 + - - +
103C LYS* 3.1 22.8 - - + +
104C TYR* 3.2 25.8 - - + -
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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
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69C THR* 4.3 2.2 - - + -
70C PHE 3.9 2.5 - - - +
71C THR 3.2 29.0 + - - +
72C GLY* 3.7 11.2 - - - +
97C TRP 3.1 5.7 + - - -
98C THR* 3.5 17.5 - - - +
100C VAL* 1.3 74.5 - - - +
102C ARG* 1.3 56.8 + - - +
104C TYR* 2.9 8.1 + - - +
105C TRP* 2.9 49.0 + - + -
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Residues in contact with ARG 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 THR 2.9 20.3 + - - +
99C ASN* 4.2 7.4 - - - +
100C VAL 3.3 0.2 - - - -
101C ALA* 1.3 70.3 - - - +
103C LYS* 1.3 67.5 + - - +
105C TRP* 3.5 35.0 - - + -
106C LYS* 2.9 29.9 + - - +
111C GLU* 2.9 43.6 + - - +
114C ILE 5.3 6.3 + - - -
116C LEU* 4.0 27.9 - - - +
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Residues in contact with LYS 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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29C LYS* 3.6 25.3 - - - +
33C GLU* 2.9 32.5 + - - +
99C ASN 3.2 15.8 + - - +
100C VAL* 3.1 12.3 + - + +
102C ARG* 1.3 76.5 - - - +
104C TYR* 1.3 69.4 + - + +
106C LYS* 3.7 5.9 - - - +
107C GLU* 3.1 35.9 + - + +
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Residues in contact with TYR 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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26C SER* 3.4 36.6 - - - -
29C LYS* 3.5 33.9 + - + +
30C LEU* 3.6 38.8 - - + -
33C GLU* 2.4 34.2 + - - +
76C LEU* 3.9 19.7 - - + -
100C VAL* 3.2 23.5 + - + -
101C ALA* 2.9 8.4 + - - +
103C LYS* 1.3 86.5 - - + +
105C TRP* 1.3 63.9 + - - +
106C LYS 3.2 1.1 - - - -
107C GLU* 3.7 17.3 - - - -
108C ASN* 2.7 31.8 + - - +
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Residues in contact with TRP 105 (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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69C THR* 4.1 4.5 - - + -
72C GLY 4.2 2.1 + - - -
75C SER* 2.9 27.5 + - - -
76C LEU* 3.6 21.5 - - + -
90C CYS* 4.1 10.3 - - - -
98C THR* 4.9 2.0 - - - -
101C ALA* 2.9 35.6 + - + +
102C ARG* 3.5 55.4 - - + +
104C TYR* 1.3 74.3 - - - +
106C LYS* 1.3 57.9 + - - +
108C ASN* 3.3 2.6 + - - -
109C GLY 3.0 8.0 + - - -
110C LEU* 2.9 29.8 + - - +
111C GLU* 3.9 10.8 - - + +
114C ILE* 3.4 53.6 - - + +
116C LEU* 4.2 28.3 - - + -
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Residues in contact with LYS 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 ARG* 2.9 21.3 + - - +
103C LYS* 3.7 6.5 - - - +
105C TRP* 1.3 73.3 - - - +
107C GLU* 1.3 65.6 + - - +
108C ASN 3.1 1.6 - - - -
109C GLY* 3.1 14.0 + - - +
111C GLU* 2.8 42.5 + - - +
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Residues in contact with GLU 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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26C SER* 2.8 29.4 + - - +
29C LYS* 2.8 36.3 + - - +
103C LYS* 3.1 29.3 + - + +
104C TYR* 3.3 22.2 + - - +
106C LYS* 1.3 75.1 - - - +
108C ASN* 1.3 60.3 + - - +
109C GLY 3.8 0.2 + - - -
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Residues in contact with ASN 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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24C PRO* 4.8 3.6 - - - +
26C SER* 2.9 34.7 + - - -
27C PHE* 3.6 23.9 - - + -
76C LEU* 3.8 11.3 - - - +
104C TYR 2.7 28.3 + - - +
105C TRP 4.0 0.4 - - - +
107C GLU* 1.3 76.7 - - - +
109C GLY* 1.3 63.3 + - - +
110C LEU* 3.3 31.1 + - + +
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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