Contacts of the strand formed by residues 59 - 66 (chain C) in PDB entry 4X4R
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 GLU 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C SER* 4.3 1.7 + - - -
48C TYR* 3.4 15.9 - - - +
53C TRP* 5.2 2.4 - - - +
57C SER 3.4 7.0 + - - +
58C LEU* 1.3 78.5 - - - +
60C ILE* 1.3 71.4 + - - +
61C ASP* 2.9 23.8 - - - +
101C HIS* 5.5 3.1 - - + -
108C GLU* 3.7 17.7 - - + +
110C ASP* 3.0 26.4 - - - +
501C APC 3.2 14.5 + - - +
502C MG 3.0 29.7 - - - -
37D C 3.1 8.3 + - - +
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Residues in contact with ILE 60 (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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24C GLY 3.6 24.7 - - - +
27C ALA* 4.2 1.8 - - + -
28C GLU* 4.2 10.5 - - - +
31C LEU* 4.4 4.5 - - + -
44C PHE* 3.3 36.1 - - + -
48C TYR* 3.7 30.5 - - + -
58C LEU* 4.7 1.1 - - + -
59C GLU* 1.3 75.5 - - - +
61C ASP* 1.3 64.7 + - - +
62C VAL* 4.2 6.1 - - + -
107C VAL* 3.9 29.4 - - + -
108C GLU 2.9 11.0 + - - +
109C VAL* 3.4 10.3 - - + +
110C ASP 3.0 24.9 + - - +
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Residues in contact with ASP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 3.6 5.7 - - - -
45C VAL* 3.2 45.2 + - + +
46C GLY* 4.2 6.1 - - - -
48C TYR* 4.9 0.2 - - - +
59C GLU* 2.9 13.4 + - - +
60C ILE* 1.3 75.6 - - - +
62C VAL* 1.3 65.9 + - - +
63C PHE* 5.0 0.9 - - + -
110C ASP* 3.5 11.7 - - - +
501C APC 3.5 6.8 + - - -
502C MG 2.6 28.6 - - - -
37D C 2.7 40.9 + - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.3 9.6 - - + -
35C LEU* 3.8 25.8 - - + -
42C TYR* 4.2 7.0 - - + -
43C VAL 3.5 9.4 - - - +
44C PHE* 3.3 41.7 - - + -
60C ILE* 4.2 5.2 - - + -
61C ASP* 1.3 74.7 - - - +
63C PHE* 1.3 71.7 + - - +
64C LEU* 4.0 6.9 + - + -
109C VAL* 5.0 4.3 - - + -
110C ASP 3.0 10.5 + - - +
111C VAL* 3.4 12.9 - - + +
112C VAL 2.9 24.3 + - - -
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Residues in contact with PHE 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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42C TYR* 3.1 7.8 - - - +
43C VAL* 2.9 51.9 + - + +
45C VAL* 3.6 22.9 - - + -
61C ASP* 5.0 0.7 - - + -
62C VAL* 1.3 77.5 - - - +
64C LEU* 1.3 60.6 - - - +
65C LEU 4.0 0.2 + - - -
112C VAL* 3.2 28.5 - - + -
114C CYS* 3.5 27.8 - - + -
127C VAL* 3.5 32.5 - - + -
130C THR* 3.6 9.0 - - - -
131C PRO* 4.1 8.3 - - + -
37D C 3.2 45.1 - + - -
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Residues in contact with LEU 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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35C LEU* 4.1 20.4 - - + -
40C VAL* 4.6 7.9 - - + -
41C GLU 3.7 2.7 - - - +
42C TYR* 3.8 21.3 - - + -
62C VAL* 4.4 3.4 - - + -
63C PHE* 1.3 73.7 - - - +
65C LEU* 1.3 61.9 + - - +
66C PHE* 3.8 17.2 + - + -
79C GLY* 3.8 23.1 - - - +
82C ILE* 3.8 24.9 - - + -
111C VAL* 3.6 31.0 - - + -
112C VAL 2.8 15.2 + - - +
113C PRO* 3.7 3.7 - - + +
114C CYS* 2.9 29.3 + - - +
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Residues in contact with LEU 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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41C GLU* 2.8 44.5 + - + +
42C TYR* 3.6 35.4 - - - +
43C VAL* 3.7 15.3 - - + -
63C PHE 4.1 0.9 - - - +
64C LEU* 1.3 71.2 - - - +
66C PHE* 1.3 68.8 + - - +
67C PRO* 4.7 1.2 - - - +
114C CYS* 3.6 18.6 - - - -
116C LYS* 3.9 34.9 - - + +
131C PRO* 4.7 16.8 - - + -
135C LYS* 5.6 6.3 - - - +
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Residues in contact with PHE 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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40C VAL* 3.8 24.9 - - + -
64C LEU* 4.1 16.6 - - + -
65C LEU* 1.3 83.0 - - - +
67C PRO* 1.3 77.1 - - + +
70C PHE* 3.6 28.5 - + + -
75C LEU* 3.6 30.5 - - + -
78C ARG* 3.8 12.6 - - + -
79C GLY* 3.7 26.7 - - - -
82C ILE* 3.6 23.8 - - + -
113C PRO* 4.9 2.0 - - + -
114C CYS 3.0 7.6 + - - -
115C TYR* 3.5 4.7 - - - -
116C LYS* 3.1 24.7 + - - +
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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