Contacts of the helix formed by residues 43 - 58 (chain B) in PDB entry 5HNK
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 PHE 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B GLY 4.4 1.3 - - - -
34B PHE* 3.4 56.1 - + + -
41B LYS 4.6 4.9 - - - +
42B PRO* 1.3 73.2 - - - +
44B ALA* 1.3 56.5 + - - +
45B SER 3.3 2.9 - - - -
46B SER* 3.0 11.5 + - - -
47B TYR* 2.7 40.5 + + + +
104B PHE* 3.7 34.5 - + - -
107B TYR* 3.5 27.6 - + + +
108B LEU* 3.8 27.8 - - + -
111B ALA* 4.1 17.9 - - + -
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Residues in contact with ALA 44 (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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42B PRO* 3.7 7.8 - - + +
43B PHE* 1.3 78.0 - - - +
45B SER* 1.3 62.1 + - - +
47B TYR* 3.5 2.3 + - - +
48B VAL* 3.3 28.4 + - - +
107B TYR 4.6 1.9 + - - +
110B ASP* 3.9 13.7 - - + +
111B ALA* 3.6 36.1 - - + +
114B LEU* 3.9 15.3 - - + +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE 3.3 0.4 - - - -
44B ALA* 1.3 78.3 - - - +
46B SER* 1.3 58.4 + - - +
48B VAL* 3.4 4.7 + - - +
49B SER* 3.0 34.9 + - - -
114B LEU* 3.9 14.7 - - - +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 5.4 0.3 + - - -
34B PHE* 3.6 17.5 - - - -
43B PHE* 3.0 14.4 + - - -
45B SER* 1.3 76.2 - - - +
47B TYR* 1.3 55.8 + - - +
48B VAL 3.4 0.2 - - - -
49B SER* 3.9 6.5 - - - -
50B THR* 2.7 40.1 + - - -
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Residues in contact with TYR 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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27B GLY* 2.7 43.4 + - - -
30B LEU* 4.2 10.4 - - + +
31B GLY* 3.8 17.0 - - - -
34B PHE* 3.6 31.4 - + + -
43B PHE* 2.7 23.5 + + + +
44B ALA 3.6 4.9 - - - +
46B SER* 1.3 72.9 - - - +
48B VAL* 1.3 66.5 + - + +
50B THR* 3.4 4.7 + - - -
51B ILE* 3.2 44.6 + - + +
65B VAL* 4.4 1.6 - - - +
108B LEU* 4.2 8.1 - - + -
111B ALA* 3.7 36.6 - - + -
112B PHE* 4.2 10.7 - + - -
115B CYS* 4.3 9.6 - - + -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 3.3 16.8 + - - +
45B SER* 3.4 4.7 + - - +
47B TYR* 1.3 76.0 - - + +
49B SER* 1.3 65.7 + - - +
51B ILE* 3.2 8.6 + - - +
52B GLN* 3.1 27.3 + - - +
111B ALA 4.0 6.1 - - - +
114B LEU* 4.0 11.7 - - + +
115B CYS* 3.6 33.4 - - + +
118B THR* 4.3 20.4 - - + +
119B PHE* 4.1 20.1 - - + -
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Residues in contact with SER 49 (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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45B SER* 3.0 21.6 + - - -
46B SER* 3.9 7.9 - - - -
48B VAL* 1.3 77.2 - - - +
50B THR* 1.3 55.8 + - - +
52B GLN* 3.4 19.1 + - - +
53B SER* 2.9 28.6 + - - -
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Residues in contact with THR 50 (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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30B LEU* 4.9 7.2 - - + -
33B ARG* 3.4 44.9 + - - +
34B PHE* 3.5 8.4 - - + -
46B SER* 2.7 24.5 + - - -
47B TYR 3.5 5.4 - - - -
49B SER* 1.3 72.9 - - - +
51B ILE* 1.3 59.2 + - - +
53B SER* 3.4 7.7 + - - -
54B LEU* 2.9 44.8 + - + +
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Residues in contact with ILE 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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23B MET* 3.6 5.7 - - + +
25B VAL* 4.3 7.6 - - + -
30B LEU* 3.6 25.4 - - + -
47B TYR* 3.2 40.8 + - + +
48B VAL* 3.2 9.6 + - - +
50B THR* 1.3 77.4 - - - +
52B GLN* 1.3 55.1 + - - +
54B LEU* 3.2 9.6 + - + +
55B ALA* 2.8 28.6 + - - +
63B THR* 3.9 19.5 - - + -
65B VAL* 4.2 9.9 - - + -
115B CYS* 4.1 15.9 - - - -
119B PHE* 3.5 23.6 - - + -
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Residues in contact with GLN 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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48B VAL* 3.1 21.0 + - - +
49B SER* 3.4 25.2 + - - +
51B ILE* 1.3 76.5 - - - +
53B SER* 1.3 60.8 + - - +
55B ALA* 3.3 6.7 + - - +
56B LYS* 3.1 30.9 + - + +
118B THR* 4.3 15.8 - - - +
119B PHE* 3.6 22.2 - - + -
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Residues in contact with SER 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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49B SER 2.9 18.0 + - - -
50B THR* 3.6 9.4 - - - -
52B GLN* 1.3 71.6 - - - +
54B LEU* 1.3 61.5 + - - +
56B LYS* 3.4 12.9 + - - +
57B SER* 3.0 34.0 + - - -
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Residues in contact with LEU 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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23B MET* 3.7 15.0 - - + -
25B VAL* 5.7 0.7 - - + -
30B LEU* 4.7 11.4 - - + -
50B THR* 2.9 35.7 + - + +
51B ILE* 3.5 10.8 - - + +
53B SER* 1.3 72.5 - - - +
55B ALA* 1.3 65.9 + - - +
57B SER* 3.1 5.9 + - - +
58B TYR* 3.0 41.4 + - + +
150B ILE* 3.9 26.5 - - + -
167B PHE* 4.1 29.8 - - + -
169B PHE* 6.5 0.4 - - + -
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Residues in contact with ALA 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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23B MET* 3.5 11.3 - - + +
51B ILE 2.8 14.4 + - - +
52B GLN* 3.4 12.8 - - - +
53B SER 3.3 0.2 - - - -
54B LEU* 1.3 76.4 - - - +
56B LYS* 1.3 61.8 + - + +
58B TYR 3.4 0.7 + - - -
59B SER 3.1 4.2 + - - -
60B ALA* 2.9 39.5 + - + +
63B THR* 3.6 22.7 - - + +
119B PHE* 5.3 4.5 - - + -
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Residues in contact with LYS 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 GLN* 3.1 21.9 + - + +
53B SER* 3.7 11.4 + - - +
55B ALA* 1.3 77.9 - - + +
57B SER* 1.3 61.6 + - - +
59B SER* 3.2 14.9 + - - +
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Residues in contact with SER 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 SER* 3.0 19.9 + - - -
54B LEU* 3.1 12.6 + - - +
56B LYS* 1.3 76.0 - - - +
58B TYR* 1.3 79.1 + - - +
59B SER* 3.5 2.6 + - - -
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Residues in contact with TYR 58 (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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21B ASN* 2.7 32.0 + - - +
23B MET* 4.5 7.9 - - + -
54B LEU* 3.0 37.0 + - + +
55B ALA 4.5 0.7 - - - +
57B SER* 1.3 88.0 - - - +
59B SER* 1.3 61.9 + - - +
60B ALA* 3.2 4.3 + - + +
148B TRP* 3.4 51.8 - + + +
150B ILE* 4.3 13.9 - - + -
167B PHE* 3.1 47.0 - + + +
174B GLU* 2.9 28.7 + - - +
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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