Contacts of the strand formed by residues 44 - 52 (chain C) in PDB entry 4F9P
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 GLY 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS 4.8 0.2 - - - -
39C GLN* 3.5 5.4 - - - +
40C ARG 2.7 31.9 + - - +
41C PRO* 4.2 5.1 + - - -
42C GLY 3.3 3.4 + - - -
43C GLN* 1.3 78.3 - - - +
45C LEU* 1.3 59.7 + - - +
46C GLU* 5.3 0.2 - - - -
223C PHE* 5.6 9.6 - - - -
236C THR* 6.0 3.1 - - - -
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Residues in contact with LEU 45 (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 ILE* 3.4 36.8 - - + -
38C LYS 3.6 11.9 - - - +
39C GLN* 4.5 9.2 - - + -
43C GLN 3.3 3.7 + - - +
44C GLY* 1.3 75.0 - - - +
46C GLU* 1.3 69.6 + - - +
105C TRP* 5.6 2.5 - - + -
172C TYR* 6.2 0.9 - - + -
174C GLN* 4.9 6.5 - - - +
180C PRO* 5.2 7.6 - - + -
223C PHE* 4.2 40.4 - - + -
234C PHE* 3.1 46.7 - - + +
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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
----------------------------------------------------------
37C ILE* 3.1 5.4 - - - +
38C LYS* 2.7 46.8 + - + +
43C GLN* 3.9 30.6 - - + +
44C GLY 5.3 0.2 - - - -
45C LEU* 1.3 80.9 - - - +
47C TRP* 1.3 62.7 + - - +
48C ILE 4.2 0.2 - - - -
61C ASN* 5.7 1.3 - - - +
64C PHE* 3.9 24.6 - - + -
234C PHE* 4.2 6.3 - - - -
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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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35C HIS* 3.0 33.7 + + + +
36C TRP 3.1 18.1 + - - -
37C ILE* 3.4 17.5 - - + -
46C GLU* 1.3 74.3 - - - +
48C ILE* 1.3 62.7 + - - +
49C GLY* 3.2 20.4 + - - -
50C VAL* 3.0 28.9 - - + -
59C HIS 3.9 10.3 - - - -
60C TYR 4.4 2.5 - - - -
61C ASN* 2.5 52.5 + - - +
64C PHE* 4.8 2.7 - - - -
225C GLN* 5.8 1.3 - - - -
230C TRP* 3.5 33.0 - + - -
231C PRO* 4.8 1.8 - - + -
232C HIS* 4.3 45.0 + - + +
234C PHE* 4.3 8.0 - + + -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TRP* 3.1 17.2 + - + +
37C ILE* 4.7 1.1 - - - +
38C LYS* 5.8 4.9 - - + +
46C GLU 4.1 1.0 + - - -
47C TRP* 1.3 77.3 - - - +
49C GLY* 1.3 57.4 + - - +
60C TYR* 3.5 3.3 - - - +
61C ASN* 2.7 32.6 + - - +
64C PHE* 3.3 36.2 - - + +
68C THR* 4.8 10.3 - - - -
81C MET* 5.1 6.3 - - - -
83C LEU* 6.4 0.4 - - + -
94C TYR* 6.3 2.2 - - + -
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Residues in contact with GLY 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 HIS* 3.4 0.5 - - - -
36C TRP* 3.0 31.1 + - - +
47C TRP* 3.2 18.6 - - - -
48C ILE* 1.3 82.2 - - - +
50C VAL* 1.3 57.7 + - - +
59C HIS 3.6 7.4 - - - -
60C TYR* 4.4 4.9 - - - -
68C THR* 6.0 0.9 - - - -
70C LEU* 3.9 17.7 - - - -
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Residues in contact with VAL 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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52A ASP* 5.3 6.7 - - + +
33C LEU* 4.3 16.2 - - + -
34C ILE 2.9 22.2 - - - +
35C HIS* 2.9 34.1 - - + +
36C TRP* 5.0 0.7 - - - -
47C TRP* 3.0 19.5 - - + -
49C GLY* 1.3 72.1 - - - +
51C ILE* 1.3 75.3 + - - +
52C ASN* 4.1 2.2 - - + +
58C SER* 3.2 25.8 - - - -
59C HIS* 3.1 20.0 + - + +
70C LEU* 3.5 8.9 - - - +
230C TRP* 5.5 6.5 - - + +
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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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34C ILE* 3.2 39.9 + - + +
36C TRP* 5.4 0.9 - - - +
50C VAL* 1.3 82.7 - - - +
52C ASN* 1.3 58.7 + - - +
53C PRO* 2.4 33.5 - - + +
56C GLY* 4.6 7.0 - - - -
57C ASP 3.2 29.6 - - - +
58C SER* 4.1 9.4 - - - -
70C LEU* 4.3 20.4 - - + +
71C THR* 4.9 1.8 - - - +
72C ALA* 3.9 32.5 - - + +
79C ALA* 4.9 1.3 - - + -
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Residues in contact with ASN 52 (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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33A THR* 5.4 2.9 - - - +
52A ASP* 2.8 40.6 - - + +
33C LEU* 3.4 19.3 - - + -
50C VAL* 4.1 2.0 - - - +
51C ILE* 1.3 71.3 - - - +
53C PRO* 1.3 68.9 - - - +
55C SER* 3.1 19.0 + - - -
56C GLY* 3.4 10.4 + - - -
57C ASP 2.8 14.7 + - - +
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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