Contacts of the strand formed by residues 42 - 51 (chain f) in PDB entry 4PJO
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 42 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28d PRO* 3.8 4.3 - - - -
78e MET* 5.2 1.6 - - + -
80e LYS* 5.0 3.1 - - + -
11f LEU* 4.7 6.3 - - + -
21f VAL* 3.9 32.1 - - - -
33f LEU* 4.4 3.4 - - + -
35f SER 3.7 4.3 - - - +
36f VAL* 4.3 13.7 - - + -
40f MET* 3.5 24.2 + - + +
41f ASN* 1.3 78.8 - - - +
43f GLN* 1.3 59.3 + - - +
44f LEU* 4.3 12.6 - - + -
62f VAL 3.5 1.6 - - - +
63f LEU* 3.5 2.0 - - - -
64f ILE* 2.7 48.7 + - + +
69f VAL* 3.9 25.6 - - + -
72f ILE* 3.9 28.0 - - + -
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Residues in contact with GLN 43 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26d THR 4.4 1.4 - - - +
27d GLY 3.6 1.4 - - - +
28d PRO* 3.4 12.6 - - + +
30d SER* 3.1 23.6 + - - -
31d VAL* 3.9 13.4 - - + +
33f LEU* 3.6 2.9 - - - +
34f VAL* 3.0 48.9 + - + +
35f SER* 2.6 40.1 + - - +
42f MET* 1.3 72.3 - - - +
44f LEU* 1.3 71.6 + - - +
45f ALA* 6.0 0.2 - - - +
61f GLU* 3.1 31.1 + - - +
62f VAL 3.3 4.9 - - - -
63f LEU* 4.6 1.1 - - - +
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Residues in contact with LEU 44 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19f VAL* 4.5 4.3 - - + -
21f VAL* 4.2 15.3 - - + -
29f TYR* 3.8 18.4 - - + +
31f GLY* 3.8 23.6 - - - +
32f TYR 3.6 4.7 - - - +
33f LEU* 4.1 20.9 - - + -
34f VAL* 4.0 2.7 - - - -
42f MET* 4.3 12.8 - - + -
43f GLN* 1.3 84.6 - - - +
45f ALA* 1.3 61.7 + - - +
47f THR* 3.0 33.4 - - + +
61f GLU* 3.5 8.3 - - - +
62f VAL* 2.9 31.8 + - + +
64f ILE* 4.1 13.5 - - + -
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Residues in contact with ALA 45 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31f GLY* 3.4 0.9 - - - -
32f TYR* 2.8 37.3 + - + +
34f VAL* 3.6 19.3 - - + -
44f LEU* 1.3 75.1 - - - +
46f ASN* 1.3 75.9 + - + +
47f THR* 3.1 3.4 + - - -
60f GLY 4.1 2.5 - - - -
61f GLU* 4.5 8.3 - - + +
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Residues in contact with ASN 46 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30f LYS 3.6 6.1 - - - +
31f GLY* 4.0 2.8 - - - -
32f TYR* 4.0 24.0 - - + -
45f ALA* 1.3 77.7 - - - +
47f THR* 1.3 62.9 + - - +
48f GLU* 3.7 4.7 + - - +
58f HIS* 3.5 32.2 + - - +
60f GLY* 3.7 8.7 + - - -
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Residues in contact with THR 47 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29f TYR* 3.8 21.8 - - + -
30f LYS 3.1 12.3 - - - +
44f LEU* 3.0 46.2 + - + +
45f ALA 3.4 1.1 + - - -
46f ASN* 1.3 75.2 - - - +
48f GLU* 1.3 65.1 + - - +
58f HIS* 3.9 2.8 - - - -
59f LEU* 2.9 25.1 + - + -
60f GLY 2.7 28.5 + - - +
62f VAL* 3.8 19.9 - - + +
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Residues in contact with GLU 48 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28f GLU 3.8 0.2 - - - +
29f TYR* 3.4 5.8 - - - -
30f LYS* 2.8 52.4 + - + +
46f ASN 4.3 5.4 - - - +
47f THR* 1.3 77.1 - - - +
49f GLU* 1.3 62.7 + - - +
50f TYR* 2.8 29.6 + - + -
55f LEU* 3.2 23.7 - - + +
57f GLY 3.2 13.7 - - - +
58f HIS* 4.0 19.8 - - + +
59f LEU* 4.3 2.0 - - - +
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Residues in contact with GLU 49 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27f MET* 5.1 2.5 - - + -
28f GLU 3.6 4.5 - - - +
29f TYR* 2.6 39.9 + - + -
48f GLU* 1.3 73.1 - - - +
50f TYR* 1.3 63.0 + - - +
51f ILE* 4.2 7.0 - - + +
55f LEU* 3.8 1.2 - - - +
56f SER* 2.7 42.2 + - - -
57f GLY 2.9 9.9 + - - +
59f LEU* 3.7 16.4 - - + +
40k GLY* 3.3 11.0 - - - -
41k ILE* 3.1 22.0 + - - +
42k ALA* 2.8 35.0 + - + +
43k PRO* 4.3 0.3 - - - +
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Residues in contact with TYR 50 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20f MET* 3.7 16.2 - - + -
27f MET* 3.6 2.9 - - - +
28f GLU* 2.8 60.5 + - + +
30f LYS* 3.2 32.0 + - + -
48f GLU* 2.8 40.6 + - + -
49f GLU* 1.3 76.1 - - - +
51f ILE* 1.3 62.9 - - - +
52f ASP 4.0 0.3 + - - -
53f GLY 3.6 16.6 - - - +
54f ALA* 3.8 4.7 - - - +
55f LEU* 3.3 41.6 - - + +
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Residues in contact with ILE 51 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27f MET* 4.2 20.6 - - + +
49f GLU* 4.2 8.5 - - + +
50f TYR* 1.3 74.4 - - - +
52f ASP* 1.3 77.7 + - + +
54f ALA* 2.9 20.8 + - - +
56f SER* 4.0 26.1 - - - +
39k CYS* 4.7 8.3 - - + -
40k GLY* 3.7 25.1 - - - +
43k PRO* 6.1 2.7 - - + -
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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