Contacts of the helix formed by residues 45 - 60 (chain B) 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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ARG* 5.3 0.2 - - - +
44B ILE* 1.3 82.3 - - - +
46B PRO* 1.3 74.5 - - - +
47B GLU* 3.3 17.4 + - - +
48B GLU* 3.4 18.2 + - - +
49B GLY* 3.1 17.7 + - - -
73B TYR* 4.1 1.9 - - - -
221B ILE* 6.0 0.5 - - - +
222B ALA* 4.9 8.0 - - - +
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Residues in contact with PRO 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 4.1 13.0 - - + -
21B VAL* 4.0 20.0 - - + -
23B GLU* 4.0 10.1 - - + +
31B ARG* 3.9 33.4 - - - +
45B SER* 1.3 86.9 - - - +
47B GLU* 1.3 74.5 + - - +
49B GLY* 3.4 1.7 + - - -
50B GLN* 3.1 29.2 + - - +
73B TYR* 3.6 23.7 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 4.4 4.2 - - - +
16B ILE* 4.4 21.2 - - + +
17B PHE* 3.6 28.6 + - - +
20B SER* 4.4 3.8 - - - +
21B VAL* 3.9 19.7 - - + -
45B SER* 3.3 22.4 - - - +
46B PRO* 1.3 77.5 - - - +
48B GLU* 1.3 68.2 + - - +
50B GLN* 2.9 8.0 + - - +
51B PHE* 2.9 21.3 + - - +
221B ILE* 4.8 12.2 - - + +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.3 35.3 - - + +
45B SER* 3.4 18.9 + - - +
47B GLU* 1.3 76.2 - - - +
49B GLY* 1.3 57.3 + - - +
51B PHE* 3.0 13.9 - - + +
52B LEU* 2.8 36.3 + - + +
152B PHE* 4.1 9.9 - - - -
180B ASP* 2.5 29.5 - - - +
221B ILE* 4.5 9.9 - - + +
222B ALA* 3.5 25.5 - - + +
225B VAL* 3.6 14.9 - - + +
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.6 12.5 - - - +
45B SER 3.1 11.3 + - - -
46B PRO 3.4 4.7 + - - -
47B GLU 3.1 1.2 - - - -
48B GLU* 1.3 77.6 - - - +
50B GLN* 1.3 56.0 + - - +
52B LEU* 3.4 1.7 + - - -
53B ASN* 2.9 27.8 + - - +
73B TYR* 4.3 2.0 - - - -
77B CYS* 3.6 32.1 - - - +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 2.7 35.1 + - - +
21B VAL* 3.5 11.0 - - + +
22B ARG* 2.8 34.8 + - - +
23B GLU* 4.9 0.9 - - - -
46B PRO 3.1 14.7 + - - +
47B GLU* 2.9 8.9 + - - +
49B GLY* 1.3 73.9 - - - +
51B PHE* 1.3 60.6 + - - +
53B ASN* 3.6 7.8 - - - +
54B ILE* 3.0 32.1 + - - +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU 2.9 11.0 + - - +
48B GLU* 3.0 18.6 - - + +
50B GLN* 1.3 75.8 - - - +
52B LEU* 1.3 61.8 + - + +
54B ILE* 3.3 14.2 - - + +
55B LEU* 3.0 62.0 + - + +
219B VAL* 4.5 18.2 - - + -
221B ILE* 4.0 35.4 - - + -
225B VAL* 4.1 21.5 - - + -
227B LEU* 4.2 15.9 - - + -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.8 28.9 - - + -
48B GLU* 2.8 27.8 + - + +
49B GLY* 3.8 4.9 - - - +
51B PHE* 1.3 78.8 - - + +
53B ASN* 1.3 60.8 + - - +
55B LEU* 3.9 4.6 - - - +
56B THR* 2.7 35.1 + - - -
74B SER* 4.0 18.2 - - - -
77B CYS* 4.7 4.5 - - + -
78B PHE* 4.0 23.5 - - + -
152B PHE* 4.0 17.3 - - + -
178B ILE* 3.8 36.6 - - + -
225B VAL* 5.3 0.2 - - + -
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Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 5.8 1.8 - - - -
49B GLY 2.9 18.8 + - - +
50B GLN* 3.6 10.3 - - - +
52B LEU* 1.3 77.3 - - - +
54B ILE* 1.3 62.6 + - - +
56B THR* 3.2 12.5 + - - -
57B LYS* 3.3 39.1 + - - +
77B CYS* 3.3 26.8 + - + +
80B SER* 4.0 11.9 + - - -
81B ALA* 3.5 14.9 - - - +
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN 3.0 16.1 + - - +
51B PHE* 3.3 22.2 - - + +
53B ASN* 1.3 79.5 + - - +
55B LEU* 1.3 63.8 + - + +
57B LYS* 3.2 10.0 + - + +
58B ILE* 2.9 53.3 + - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B PHE* 3.0 43.6 + - + +
52B LEU* 3.9 4.0 - - - +
54B ILE* 1.3 82.8 - - + +
56B THR* 1.3 57.2 + - - +
58B ILE* 4.0 17.6 - - + +
59B SER* 3.0 32.1 + - - -
150B LEU* 4.6 2.5 - - - +
176B LEU* 4.9 9.8 - - + +
178B ILE* 3.9 23.1 - - + -
227B LEU* 3.7 39.7 - - + -
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU 2.7 19.4 + - - -
53B ASN 3.2 9.2 + - - -
55B LEU* 1.3 76.5 - - - +
57B LYS* 1.3 61.6 + - - +
59B SER* 2.9 19.9 + - - -
60B GLY* 3.3 6.4 + - - -
61B ALA* 3.6 7.9 + - + +
64B ILE* 3.7 25.6 - - + +
78B PHE* 3.2 25.4 - - - +
81B ALA* 3.8 19.8 - - + +
82B LEU* 3.8 18.4 - - + +
83B PRO* 5.8 0.2 - - + -
150B LEU* 4.4 5.8 - - - +
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ASN* 3.4 34.0 + - - +
54B ILE* 3.2 10.9 + - + +
56B THR* 1.3 75.6 - - - +
58B ILE* 1.3 66.5 + - + +
60B GLY* 3.1 14.5 + - - -
80B SER 4.9 2.8 + - - -
81B ALA* 3.8 30.1 - - - +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 2.9 50.7 + - + +
55B LEU* 4.0 16.6 - - + +
57B LYS* 1.3 73.6 - - + +
59B SER* 1.3 63.2 + - - +
60B GLY* 3.3 1.0 + - - -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU 3.0 16.3 + - - -
56B THR* 2.9 19.1 + - - -
58B ILE* 1.3 77.5 - - - +
60B GLY* 1.3 59.7 + - - +
61B ALA* 3.1 19.5 + - - +
150B LEU* 3.8 9.5 - - - +
176B LEU* 4.8 13.0 - - - -
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR 3.3 1.9 + - - -
57B LYS 3.1 16.1 + - - -
58B ILE 3.2 1.6 + - - -
59B SER* 1.3 77.9 + - - +
61B ALA* 1.3 68.4 + - - +
62B LYS* 3.4 15.1 + - - +
83B PRO* 5.6 1.1 - - - +
149B ASP* 4.9 1.4 - - - +
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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