Contacts of the strand formed by residues 58 - 66 (chain C) in PDB entry 5EWL
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 ILE 58 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PRO* 3.6 0.2 - - - +
25C LYS* 3.6 12.1 - - + +
27C VAL* 3.7 18.6 - - + -
54C PHE 3.3 17.4 - - - +
55C THR* 3.2 11.9 - - - +
56C ARG 3.3 2.6 + - - +
57C LYS* 1.3 84.8 - - + +
59C GLN* 1.4 62.1 + - - +
313C ILE* 3.7 19.7 - - + +
314C HIS* 3.7 38.2 + - + +
317C PHE* 3.6 46.0 - - + -
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Residues in contact with GLN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PRO* 3.9 21.5 - - + +
25C LYS 2.9 12.8 + - - +
26C ILE* 3.3 26.1 - - + +
27C VAL* 2.9 27.2 + - - -
50C ASN* 3.5 16.8 - - - +
55C THR* 3.4 30.5 - - + +
58C ILE* 1.4 74.9 - - - +
60C LEU* 1.3 72.6 + - - +
61C GLN* 5.6 1.8 + - - -
314C HIS* 5.4 1.1 - - - -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 3.2 27.4 - - + +
29C ILE* 3.5 30.7 - - + -
46C VAL* 4.0 16.2 - - + +
49C ALA* 4.0 15.0 - - + -
50C ASN* 3.0 27.4 + - - +
58C ILE* 5.2 1.6 - - + -
59C GLN* 1.3 86.1 + - - +
61C GLN* 1.3 62.4 + - - +
306C VAL* 5.6 1.1 - - + -
310C ALA* 3.7 31.6 - - + -
313C ILE* 4.1 18.2 - - + -
314C HIS* 4.8 11.4 - - + -
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Residues in contact with GLN 61 (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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26C ILE* 3.5 35.2 - - + +
27C VAL 3.1 5.7 + - - -
28C ASN* 3.2 30.7 + - - +
29C ILE* 2.9 24.9 + - - -
46C VAL* 4.1 3.8 - - - -
59C GLN* 5.6 2.2 + - - +
60C LEU* 1.3 75.7 - - - +
62C ALA* 1.3 70.3 + - - +
63C THR* 3.7 0.8 + - - +
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Residues in contact with ALA 62 (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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29C ILE 3.6 5.2 - - - -
42C PHE* 3.6 23.1 - - + -
43C ARG* 4.1 22.4 - - + +
46C VAL* 3.6 28.2 - - + +
61C GLN* 1.3 82.2 - - - +
63C THR* 1.3 58.8 + - - +
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Residues in contact with THR 63 (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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28C ASN* 3.4 31.7 + - - +
29C ILE 2.9 9.1 + - - -
30C GLY* 3.1 4.0 - - - -
31C ALA 3.0 20.6 + - - -
42C PHE* 3.2 4.4 - - - -
61C GLN* 4.9 0.3 + - - +
62C ALA* 1.3 72.5 + - - +
64C SER* 1.3 63.6 + - - +
81C ASP 3.4 26.0 - - - +
82C LEU* 3.8 10.3 - - + -
85C SER* 3.7 17.6 - - - +
87C VAL* 4.2 7.6 - - - -
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Residues in contact with SER 64 (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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31C ALA* 3.2 15.7 - - - -
33C LEU* 4.8 1.3 - - - -
39C GLU* 2.7 44.2 + - - +
42C PHE* 3.8 21.4 - - - -
43C ARG* 5.7 2.1 + - - +
62C ALA 4.4 0.2 - - - -
63C THR* 1.3 79.9 - - - +
65C VAL* 1.3 72.6 + - - +
82C LEU* 4.0 3.6 - - - -
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Residues in contact with VAL 65 (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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31C ALA 3.0 12.2 + - - +
32C VAL* 3.3 12.0 - - + -
33C LEU* 2.9 23.9 + - - +
39C GLU* 3.4 12.1 - - - +
64C SER* 1.3 78.8 - - - +
66C THR* 1.3 68.5 + - - +
68C ARG* 4.2 8.1 - - - +
74C MET* 4.0 14.6 - - + -
77C SER* 3.7 16.6 - - - +
81C ASP* 3.4 39.5 - - + +
82C LEU* 4.4 9.0 - - + -
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Residues in contact with THR 66 (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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32C VAL* 4.3 3.0 - - - +
33C LEU 3.0 15.9 - - - +
34C SER 3.5 16.8 - - - +
35C THR* 3.6 18.6 - - - +
36C LYS* 4.0 2.5 - - + +
39C GLU* 3.6 21.8 + - - +
65C VAL* 1.3 82.0 - - - +
67C HIS* 1.3 67.2 + - - +
68C ARG* 3.3 32.8 + - - +
74C MET* 4.4 0.2 - - - +
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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