Contacts of the strand formed by residues 43 - 52 (chain L) in PDB entry 4M75
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 VAL 43 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L ILE* 4.3 6.5 - - + -
34L LEU* 3.4 22.4 - - + -
36L GLY 3.6 2.0 - - - -
37L PHE* 3.9 15.7 - - + -
41L VAL* 3.8 6.0 + - + +
42L ASN* 1.3 78.8 - - - +
44L ILE* 1.3 65.2 + - - +
45L LEU* 3.5 27.6 - - + -
71L MSE 3.7 0.2 - - - +
72L LEU* 3.5 2.3 - - - +
73L LEU* 2.6 47.4 + - + +
78L ILE* 3.7 25.1 - - + +
81L LEU* 4.3 18.8 - - + -
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Residues in contact with ILE 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 4.3 20.6 - - + +
12K THR* 4.4 7.2 - - - +
15K PHE* 4.3 27.1 - - + -
34L LEU* 3.4 8.0 - - - +
35L VAL* 2.9 42.9 + - + -
36L GLY 2.6 30.5 + - - +
37L PHE* 5.2 0.2 - - - -
38L ASP 6.1 0.2 - - - +
42L ASN 5.2 1.3 - - - +
43L VAL* 1.3 74.3 - - - +
45L LEU* 1.3 67.1 + - - +
70L ARG* 4.5 13.9 - - + -
71L MSE 3.4 10.3 - - - +
72L LEU* 3.7 26.7 - - + -
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L VAL* 4.1 11.2 - - + -
22L ILE* 4.1 19.5 - - + -
30L PHE* 4.9 1.3 - - + +
31L GLU 4.9 1.8 - - - -
32L GLY 4.0 29.2 - - - +
33L THR 3.2 9.0 - - - +
34L LEU* 4.4 1.1 - - - +
35L VAL* 4.1 4.9 - - - -
43L VAL* 3.5 19.7 - - + -
44L ILE* 1.3 77.7 - - - +
46L GLU* 1.3 60.2 + - - +
48L ALA* 4.2 7.9 - - + +
70L ARG* 3.2 5.0 - - - +
71L MSE 3.0 68.1 + - + +
73L LEU* 3.4 17.5 - - + -
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Residues in contact with GLU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L GLY* 3.6 0.3 - - - -
33L THR* 2.8 45.7 + - - +
35L VAL* 4.1 7.7 - - + +
45L LEU* 1.3 72.1 - - - +
47L ASP* 1.3 90.9 + - - +
48L ALA 3.1 3.2 + - - -
69L GLY* 3.2 20.0 - - - +
70L ARG* 3.3 35.5 + - - +
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Residues in contact with ASP 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLU 3.8 3.1 - - - +
32L GLY* 3.8 4.0 - - - -
33L THR* 6.1 0.3 - - - -
45L LEU 4.2 0.2 + - - -
46L GLU* 1.3 88.2 - - - +
48L ALA* 1.3 57.2 + - - +
49L VAL* 3.7 5.5 + - - +
66L GLN* 3.2 21.3 + - - +
67L HIS 2.7 13.9 - - - -
68L HIS* 3.5 9.0 - - - +
69L GLY 2.8 33.3 + - - +
70L ARG* 4.7 0.2 - - - +
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Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L PHE* 4.8 4.5 - - + -
31L GLU 2.9 13.0 - - - +
45L LEU* 4.2 16.4 + - + +
46L GLU 3.8 1.8 - - - -
47L ASP* 1.3 74.8 - - - +
49L VAL* 1.3 61.0 + - - +
66L GLN* 4.0 0.9 - - - -
67L HIS* 3.0 39.4 + - + +
70L ARG* 6.1 0.2 - - - +
71L MSE 3.9 37.2 - - + -
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Residues in contact with VAL 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLU 3.6 1.7 - - - +
30L PHE* 3.4 6.8 - - - -
31L GLU* 2.5 66.2 + - + +
47L ASP 4.3 4.5 - - - +
48L ALA* 1.3 73.9 - - - +
50L GLU* 1.3 59.9 + - - +
51L TRP* 2.8 41.0 - - + +
63L LYS* 5.0 2.7 - - + -
65L MSE 3.8 11.9 - - - +
66L GLN* 3.5 23.3 - - + +
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Residues in contact with GLU 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K LYS* 3.0 20.3 + - - +
80K TYR* 2.5 24.7 + - - -
28L ARG* 2.6 32.4 + - - +
30L PHE* 3.0 33.7 - - + -
48L ALA 3.8 1.2 + - - -
49L VAL* 1.3 70.5 - - - +
51L TRP* 1.3 73.4 + - - +
64L VAL* 2.7 41.3 + - + +
65L MSE 3.1 17.4 + - - +
67L HIS* 3.2 14.9 + - - +
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Residues in contact with TRP 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 6.3 1.6 - - + -
28L ARG* 3.1 6.3 - - - +
29L GLU* 2.5 65.7 + - + +
31L GLU* 4.6 21.3 - - + -
49L VAL* 2.8 36.9 - - + +
50L GLU* 1.3 107.7 - - - +
52L LEU* 1.3 59.3 + - - +
53L ILE* 4.0 7.1 + - + -
61L ASN* 5.2 15.3 - - + -
62L GLU 3.4 7.6 - - - +
63L LYS* 3.1 40.5 - - + +
64L VAL* 4.7 1.1 - - - -
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Residues in contact with LEU 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K TYR* 6.5 0.9 - - + -
26L SER* 6.2 0.9 - - - -
27L ASN* 2.9 41.5 - - - +
28L ARG* 3.9 36.6 - - - +
51L TRP* 1.3 71.9 - - - +
53L ILE* 1.3 61.7 + - - +
61L ASN 4.3 0.3 - - - -
62L GLU* 3.1 37.3 + - + +
64L VAL* 4.3 15.9 - - + +
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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