Contacts of the strand formed by residues 45 - 51 (chain C) in PDB entry 5JMO
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 LEU 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 4.1 21.1 - - + -
38C ARG 3.7 4.7 - - - +
39C GLN* 3.3 41.3 - - + +
44C GLY* 1.3 73.1 - - - -
46C GLU* 1.3 60.3 + - - +
47C TRP 4.3 0.6 + - - -
95C TYR* 4.5 13.0 - - + -
100C MET* 3.9 22.7 - - + +
101C TYR* 5.6 7.2 - - + -
102C ALA 6.0 1.3 - - - +
107C ARG* 5.6 10.5 - - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 3.3 4.0 - - - -
38C ARG* 2.7 80.3 + - + +
44C GLY 3.5 3.6 + - - +
45C LEU* 1.3 77.0 - - - +
47C TRP* 1.3 76.1 + - - +
48C VAL* 3.6 1.5 + - - +
61C ALA* 4.8 2.5 - - + +
63C SER* 3.2 24.2 + - - -
64C VAL* 6.2 0.2 - - - -
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Residues in contact with TRP 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A ALA* 3.6 31.2 - - + -
526A ASP* 5.8 3.6 - - - +
35C TYR* 4.1 7.0 - + - -
36C TRP 3.7 4.0 - - - -
37C VAL* 3.9 10.3 - - + +
45C LEU 4.3 0.4 - - - -
46C GLU* 1.3 85.6 - - - +
48C VAL* 1.3 64.8 + - - +
49C SER* 3.0 29.5 + - - -
50C SER* 3.6 23.3 - - - +
59C ASP* 3.8 21.1 - - + -
60C TYR 3.5 23.1 - - - -
61C ALA* 3.4 34.4 - - + +
100C MET* 3.4 44.2 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TRP* 2.8 21.3 + - + +
37C VAL* 4.3 1.6 - - - -
38C ARG* 3.6 46.2 - - + +
46C GLU* 3.8 2.7 - - + +
47C TRP* 1.3 80.5 - - - +
49C SER* 1.3 64.9 + - - +
60C TYR* 3.6 1.4 - - - -
61C ALA* 2.9 29.9 + - - -
64C VAL* 3.6 11.5 - - + +
68C PHE* 3.6 35.7 - - + -
81C LEU* 4.3 9.0 - - + -
94C TYR* 4.3 5.4 - - + -
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 3.5 1.0 - - - -
36C TRP* 2.9 27.8 + - - -
47C TRP* 3.0 15.5 + - - +
48C VAL* 1.3 89.5 - - - +
50C SER* 1.3 60.3 + - - +
59C ASP 2.9 19.7 + - - -
60C TYR* 3.2 14.9 - - - -
70C ILE* 3.2 33.7 - - - +
81C LEU* 4.3 8.5 - - - -
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Residues in contact with SER 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A ASN* 5.3 1.9 - - - +
560A TYR* 2.8 25.5 + - - -
34C MET 3.3 6.7 - - - -
35C TYR* 3.6 29.4 - - - -
47C TRP* 3.6 8.4 - - - -
49C SER* 1.3 78.6 + - - +
51C ILE* 1.3 62.6 + - - +
58C THR* 3.3 4.0 - - - -
59C ASP* 2.9 39.5 + - - +
70C ILE* 3.7 7.8 - - - +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A TYR* 3.5 5.8 - - - -
33C SER* 3.3 4.2 - - - -
34C MET* 3.0 36.9 + - + +
50C SER* 1.3 77.1 - - - +
52C ASN* 1.3 70.2 + - - +
55C GLY* 3.6 28.7 - - - +
57C ASN 3.3 13.5 - - - +
58C THR* 3.7 16.6 - - + -
70C ILE* 3.7 8.7 - - + +
71C SER* 3.8 27.6 - - - +
72C ARG* 4.0 13.5 - - + +
79C LEU* 3.7 28.5 - - + -
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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