Contacts of the strand formed by residues 28 - 35 (chain C) in PDB entry 4A8X
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 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 3.5 19.5 - - - +
230A GLY* 4.0 3.6 - - - +
26C CYS 3.9 0.6 + - - -
27C PRO* 1.3 72.2 - - - +
29C LEU* 1.3 75.6 + - - +
30C LEU* 3.6 14.3 + - + -
59C TYR* 3.3 7.7 - - - -
60C THR* 2.8 48.9 + - + +
61C TRP* 3.7 24.0 - - - +
62C MET* 3.8 27.1 - - + +
122C LEU* 5.0 1.6 - - + -
127C PHE* 4.2 20.2 - - + -
129C ILE* 3.9 17.0 - - + -
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASN* 3.0 32.2 + - - +
229A ASP* 2.8 18.6 + - - +
668B PRO* 3.6 37.2 - - + -
669B CYS 4.0 8.5 - - - +
670B ILE* 4.4 5.2 - - + -
28C LEU* 1.3 78.7 - - - +
30C LEU* 1.3 64.2 + - - +
31C ARG* 4.1 14.9 + - + +
57C GLN* 4.1 26.9 - - + -
58C ILE 3.7 6.5 - - - +
59C TYR* 3.9 33.1 - - + +
129C ILE* 4.7 0.9 - - - +
130C GLY* 4.8 3.1 + - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.6 9.6 + - + -
29C LEU* 1.3 75.7 - - - +
31C ARG* 1.3 64.8 + - - +
32C VAL* 3.6 22.6 + - + -
56C LEU 3.6 2.3 - - - +
57C GLN* 3.6 2.3 - - - -
58C ILE* 2.8 46.2 + - + +
60C THR* 4.2 19.1 - - + -
69C LEU* 4.2 15.0 - - + -
122C LEU* 4.9 5.2 - - + -
127C PHE* 3.5 37.2 - - + -
131C ASP 4.2 6.5 - - - +
133C LEU* 3.8 28.3 - - + -
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Residues in contact with ARG 31 (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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171A ASN* 4.1 18.7 + - - +
668B PRO* 5.0 12.4 - - - +
29C LEU* 4.1 24.4 + - + +
30C LEU* 1.3 77.5 - - - +
32C VAL* 1.3 59.8 + - - +
33C PHE* 3.8 15.0 - - + -
49C GLY 5.4 3.8 + - - -
51C VAL* 3.9 20.7 - - - +
55C GLU* 2.7 44.4 + - - +
56C LEU 3.8 2.7 - - - -
57C GLN* 4.4 4.2 - - + +
130C GLY 5.9 0.4 - - - -
131C ASP 5.0 2.6 + - - +
132C TYR* 3.8 38.6 + - + -
133C LEU* 3.2 21.8 + - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.6 32.8 - - + +
31C ARG* 1.3 76.3 - - - +
33C PHE* 1.3 71.9 + - - +
34C THR* 4.3 7.2 - - + -
54C SER 4.0 0.3 - - - +
55C GLU* 3.5 4.7 - - - +
56C LEU* 2.7 60.2 + - + +
58C ILE* 4.1 14.4 - - + -
73C VAL* 5.0 2.5 - - + -
133C LEU* 3.4 14.1 - - + +
135C ILE* 3.6 31.6 - - + -
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Residues in contact with PHE 33 (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 ARG* 3.8 21.3 - - + -
32C VAL* 1.3 77.1 - - - +
34C THR* 1.3 65.1 + - - +
41C HIS* 3.8 9.2 - - + +
46C PHE* 4.0 12.8 - + - -
51C VAL* 3.5 27.6 - - + -
52C PRO* 3.5 34.5 - - + -
53C SER 4.4 2.5 - - - +
54C SER 4.6 2.5 - - - -
55C GLU* 3.3 42.0 - - + -
132C TYR* 4.0 23.8 - + + -
133C LEU 2.9 11.2 + - - +
134C ASP* 3.4 21.0 - - - +
135C ILE 2.8 26.0 + - - -
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Residues in contact with THR 34 (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 15.0 - - + +
33C PHE* 1.3 82.5 - - - +
35C THR* 1.3 65.4 + - - +
41C HIS* 3.3 14.0 + - - -
53C SER 5.5 1.7 - - - +
54C SER* 4.7 12.6 + - - +
56C LEU* 5.1 6.7 - - + -
73C VAL* 4.9 6.1 - - + -
77C TYR* 3.7 34.5 + - + -
134C ASP* 5.4 0.2 - - - -
135C ILE* 3.2 20.2 - - + +
137C ILE* 4.2 15.7 - - + +
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Residues in contact with THR 35 (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 THR* 1.3 80.0 - - - +
36C ASN* 1.3 61.3 + - - +
37C ASN* 3.6 11.8 + - - +
39C ARG 2.8 29.5 + - - +
40C HIS* 4.5 1.6 - - - -
41C HIS* 3.5 30.3 - - + +
134C ASP* 4.9 1.6 - - - +
135C ILE 3.0 4.2 + - - +
136C ALA* 3.2 15.6 - - - +
137C ILE* 2.8 30.9 + - - +
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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