Contacts of the helix formed by residues 50 - 64 (chain K) in PDB entry 4QOC
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 MET 50 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23K GLU* 3.3 44.0 - - - +
24K GLN* 3.6 4.3 + - - +
26K THR* 2.8 17.9 + - - +
28K VAL* 4.2 21.5 - - + +
49K THR* 1.3 72.9 - - - +
51K LYS* 1.3 64.3 + - - +
53K VAL* 3.1 10.8 + - - +
54K LEU* 2.9 30.5 + - + +
100K TYR* 3.7 27.8 - - + -
103K ILE* 4.1 21.5 - - + -
104K TYR* 4.2 17.7 - - + +
107K LEU* 4.3 9.9 - - + -
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Residues in contact with LYS 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 6.3 1.9 - - + +
24K GLN* 2.9 47.4 + - + +
49K THR* 3.1 7.2 - - - +
50K MET* 1.3 77.9 - - - +
52K GLU* 1.3 63.1 + - + +
54K LEU* 3.2 5.6 + - - +
55K PHE* 3.0 21.8 + - + +
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Residues in contact with GLU 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLU* 4.2 5.9 - - - +
45K LYS* 2.6 42.3 + - - -
48K TYR* 3.5 12.8 - - + -
49K THR* 3.0 39.9 + - - +
51K LYS* 1.3 79.2 - - + +
53K VAL* 1.3 65.7 + - - +
55K PHE* 3.1 7.4 + - - +
56K TYR* 3.0 41.2 + - + -
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Residues in contact with VAL 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K VAL* 3.7 29.6 - - + -
30K PRO* 4.5 4.3 - - + -
34K LEU* 4.5 13.0 - - + -
38K LEU* 4.2 18.5 - - + +
48K TYR* 3.8 15.7 - - + -
49K THR 3.1 5.3 + - - +
50K MET* 3.1 12.4 + - - +
52K GLU* 1.3 76.8 - - - +
54K LEU* 1.3 62.0 + - - +
56K TYR* 4.0 2.2 - - - +
57K LEU* 3.0 42.5 + - + +
103K ILE* 4.4 17.7 - - + -
107K LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K GLN* 3.9 19.1 - - + +
50K MET* 2.9 27.6 + - + +
51K LYS 3.4 6.3 - - - +
53K VAL* 1.3 78.9 - - - +
55K PHE* 1.3 62.1 + - - +
57K LEU* 4.6 0.7 - - - -
58K GLY* 3.0 18.2 + - - -
99K ILE* 4.8 0.2 - - + -
100K TYR* 3.4 25.6 - - + +
103K ILE* 3.6 28.5 - - + -
201K 35T 3.5 68.6 + - + -
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Residues in contact with PHE 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K LYS* 3.0 14.0 + - + +
52K GLU* 3.1 9.8 + - - +
54K LEU* 1.3 77.2 - - - +
56K TYR* 1.3 88.0 + + - +
58K GLY* 3.2 2.4 + - - -
59K GLN* 2.8 48.7 + - + +
201K 35T 3.3 40.0 - - + -
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Residues in contact with TYR 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K LEU* 3.3 23.1 - - + -
41K VAL* 3.7 29.2 - - + +
42K GLY* 4.1 7.3 + - - -
43K ALA* 3.8 41.0 - - + -
44K GLN 4.9 0.9 + - - -
45K LYS* 6.1 0.3 - - - -
48K TYR* 4.0 20.1 - + - -
52K GLU* 3.0 39.7 + - + +
53K VAL* 4.7 0.2 - - - -
55K PHE* 1.3 94.9 - + - +
57K LEU* 1.3 60.8 + - - +
59K GLN* 3.1 5.4 + - + +
60K TYR* 2.8 30.4 + - - +
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K LEU* 4.2 18.2 - - + -
37K LEU* 4.0 20.2 - - + -
38K LEU* 4.1 3.1 - - + +
53K VAL* 3.0 30.6 + - + +
54K LEU 3.9 3.4 - - - +
56K TYR* 1.3 75.5 - - - +
58K GLY* 1.3 58.0 + - - +
60K TYR* 3.1 6.3 + - + +
61K ILE* 2.9 34.6 + - + +
82K LEU* 3.9 28.5 - - + -
85K LEU* 5.6 0.4 - - + -
86K PHE* 4.0 13.5 - - + -
103K ILE* 3.8 35.7 - - + -
201K 35T 4.0 11.2 - - + -
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Residues in contact with GLY 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K LEU 3.0 11.4 + - - -
55K PHE 3.5 4.3 - - - -
57K LEU* 1.3 78.0 - - - +
59K GLN* 1.3 56.8 + - - +
61K ILE* 3.3 3.7 + - - +
62K MET* 3.0 32.6 + - - +
201K 35T 3.5 43.3 - - - -
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Residues in contact with GLN 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K VAL* 4.7 17.9 + - + +
55K PHE* 2.8 41.5 + - + +
56K TYR* 3.1 8.9 + - + +
58K GLY* 1.3 72.7 - - - +
60K TYR* 1.3 58.0 + - - +
62K MET* 3.9 6.6 - - - +
63K THR* 2.9 46.3 + - - +
201K 35T 3.1 22.2 - - - +
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Residues in contact with TYR 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LEU* 3.7 43.5 - - + -
40K SER* 4.3 7.0 - - - -
41K VAL* 3.8 27.3 - - + +
56K TYR 2.8 13.4 + - - +
57K LEU* 3.2 10.8 - - + +
59K GLN* 1.3 76.3 - - - +
61K ILE* 1.3 70.7 + - - +
63K THR* 3.9 1.2 - - - -
64K LYS* 3.0 59.7 + - + +
66K LEU* 4.1 9.0 - - + -
80K ASP* 2.4 29.7 + - - -
81K LEU* 4.1 12.3 - - + +
82K LEU* 3.9 22.4 - - + -
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Residues in contact with ILE 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K LEU 2.9 17.0 + - - +
58K GLY 3.6 5.4 - - - +
60K TYR* 1.3 80.6 - - + +
62K MET* 1.3 60.9 + - - +
64K LYS 3.6 0.3 + - - -
65K ARG 3.2 2.8 + - - -
66K LEU* 3.0 34.1 + - + +
67K TYR* 3.3 31.8 + - + +
75K VAL* 3.7 12.8 - - + -
82K LEU* 3.5 30.3 - - + -
91K PHE* 4.2 9.4 - - + -
201K 35T 3.6 52.0 - - + -
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Residues in contact with MET 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K GLY 3.0 21.7 + - - +
59K GLN* 3.9 9.6 - - - +
61K ILE* 1.3 76.6 - - - +
63K THR* 1.3 55.2 + - - +
65K ARG* 2.7 44.9 + - - +
67K TYR* 3.6 44.1 - - + +
68K ASP* 5.4 1.6 - - - -
69K GLU* 4.8 15.3 - - + -
201K 35T 4.1 22.2 - - + -
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Residues in contact with THR 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K VAL* 5.2 8.0 - - + +
59K GLN* 2.9 35.1 + - - +
60K TYR* 4.0 4.3 - - - -
62K MET* 1.3 73.2 - - - +
64K LYS* 1.3 75.5 + - + +
65K ARG* 3.2 7.5 + - - +
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Residues in contact with LYS 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K SER* 4.6 16.2 + - - -
41K VAL* 5.2 2.0 - - - +
60K TYR* 3.0 60.0 + - + +
63K THR* 1.3 92.7 - - + +
65K ARG* 1.3 72.0 + - - +
66K LEU* 3.4 22.8 + - + +
80K ASP* 4.6 6.5 - - - +
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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