Contacts of the strand formed by residues 54 - 59 (chain C) in PDB entry 3SBW
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 54 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B LEU* 4.5 26.7 - - + +
129B HIS* 5.8 7.2 - - + -
132B LEU* 4.3 30.3 - - + -
51C ALA 5.7 1.3 - - - +
52C ALA 4.5 6.3 - - - +
53C LEU* 1.3 77.7 - - - +
55C VAL* 1.3 70.5 + - - +
56C TYR 4.3 0.2 - - - -
67C PHE 3.3 11.4 - - - +
68C VAL* 4.8 19.1 - - + -
69C HIS 5.2 1.3 - - - +
115C MET* 3.7 10.5 - - + +
116C ILE* 3.2 8.5 - - - +
117C SER* 2.9 46.9 + - - +
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Residues in contact with VAL 55 (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 PHE* 5.4 0.7 - - + -
53C LEU* 4.1 26.0 - - + -
54C ILE* 1.3 81.9 - - - +
56C TYR* 1.3 63.1 + - - +
57C TRP* 3.8 29.8 - - + +
65C ILE* 3.5 5.4 - - + +
66C GLN* 3.6 0.9 - - - -
67C PHE* 2.8 47.2 + - + +
87C LEU* 4.1 15.3 - - + -
92C LEU* 4.4 13.9 - - + -
97C ALA* 4.2 1.8 - - + -
115C MET 3.4 2.9 - - - -
116C ILE* 3.8 23.1 - - + -
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Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.7 53.3 + - + -
133B LYS* 4.5 2.8 - - - -
134B ILE* 4.1 19.6 + - + -
55C VAL* 1.3 76.0 - - - +
57C TRP* 1.3 73.8 + - - +
58C GLU* 3.6 34.0 + - + +
61C ASP* 5.6 2.3 - - - -
62C LYS 5.3 0.2 - - - -
63C ASN* 3.6 30.9 + - - +
65C ILE 3.3 13.2 - - - -
113C ARG 3.7 1.2 - - - +
114C CYS* 3.2 4.2 - - - +
115C MET* 2.7 66.6 + - + +
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Residues in contact with TRP 57 (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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38C ILE* 3.6 37.5 - - + -
40C CYS* 3.7 14.6 - - + -
55C VAL* 3.8 21.1 - - + +
56C TYR* 1.3 76.2 - - - +
58C GLU* 1.3 63.9 + - - +
64C ILE* 3.0 26.5 + - + -
65C ILE* 3.0 33.1 + - + +
87C LEU* 3.6 21.2 - - + +
97C ALA* 3.2 24.7 + - + +
99C LEU* 3.6 33.3 - - + +
112C TYR* 4.6 8.3 - + + -
113C ARG 3.4 13.2 - - - -
114C CYS* 3.5 33.9 - - + -
126C ILE* 3.9 13.5 - - + -
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Residues in contact with GLU 58 (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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134B ILE* 4.5 4.9 - - + +
56C TYR* 3.6 35.1 + - + +
57C TRP* 1.3 77.7 - - - +
59C MET* 1.3 65.2 + - - +
60C GLU 4.1 4.9 + - - -
61C ASP* 3.3 33.7 + - - +
62C LYS 3.3 12.8 - - - +
64C ILE* 4.1 5.3 - - - +
111C VAL 5.1 1.2 - - - +
112C TYR* 3.4 7.8 - - - +
113C ARG* 2.9 79.8 + - + +
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Residues in contact with MET 59 (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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58C GLU* 1.3 76.5 - - - +
60C GLU* 1.3 96.8 + - - +
61C ASP 3.3 0.7 - - - -
62C LYS* 2.8 40.6 + - - +
64C ILE* 4.0 3.6 - - + -
81C TYR* 2.7 36.3 - - - +
107C GLN 3.8 17.3 - - - +
108C ASP* 4.3 2.9 - - - +
109C ALA 4.4 8.5 - - - +
110C GLY* 4.6 3.1 - - - -
111C VAL 3.4 20.0 - - - +
112C TYR* 3.5 44.9 - - + +
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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