Contacts of the strand formed by residues 121 - 131 (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 ALA 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B MET* 3.9 29.1 - - - +
66B ASN* 3.8 6.1 + - - +
78B LYS* 2.5 36.8 + - - +
126B ILE* 4.5 9.9 - - + -
128B LEU* 5.6 1.3 - - + -
19C PHE* 3.6 4.1 - - - -
115C MET* 4.3 10.1 - - - -
116C ILE 3.3 11.0 - - - +
117C SER* 4.1 13.9 - - - +
120C GLY* 1.3 75.8 - - - +
122C ASP* 1.3 58.0 + - - +
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Residues in contact with ASP 122 (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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66B ASN* 4.3 9.9 + - - +
68B ASN* 4.8 2.6 - - - +
78B LYS* 3.9 29.8 + - - +
126B ILE* 4.6 1.7 - - - +
19C PHE* 3.9 4.9 - - + -
20C THR* 3.2 22.4 + - - -
21C VAL* 3.3 30.2 + - + +
115C MET* 3.5 5.5 - - - +
116C ILE 3.1 29.2 + - - +
121C ALA* 1.3 78.5 - - - +
123C TYR* 1.3 82.8 + - - +
124C LYS* 3.4 14.4 + - - -
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Residues in contact with TYR 123 (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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66B ASN* 4.5 8.5 - - + -
68B ASN* 2.7 31.4 + - - -
76B THR* 3.7 22.9 + - + -
122B LEU* 3.9 2.6 - - - +
124B GLY* 4.2 8.0 - - - -
126B ILE* 3.9 28.5 - - + -
134B ILE* 4.1 19.3 - - + -
136B GLU* 3.1 43.6 + - + +
21C VAL* 5.0 1.1 - - - -
113C ARG* 4.3 17.0 - - + -
114C CYS* 3.1 17.5 - - - +
115C MET* 4.1 11.9 - - + -
122C ASP* 1.3 88.3 + - - +
124C LYS* 1.3 75.3 + - - +
125C ARG* 4.9 1.1 - - - -
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Residues in contact with LYS 124 (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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75B GLN* 3.1 33.2 - - - +
76B THR* 3.3 22.2 + - - +
77B GLU* 4.5 11.2 - - - +
78B LYS 5.0 0.6 - - - +
20C THR* 4.8 2.4 + - - -
21C VAL* 3.0 37.6 + - + +
22C THR* 4.8 4.0 - - - +
23C VAL* 3.9 28.3 - - + +
40C CYS* 5.0 0.2 - - - -
112C TYR 3.8 0.2 - - - +
113C ARG* 3.3 6.8 - - - +
114C CYS* 3.1 37.7 + - - -
122C ASP* 3.4 17.6 + - - -
123C TYR* 1.3 76.7 + - - +
125C ARG* 1.3 62.8 + - - +
126C ILE* 4.1 0.6 + - - +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.0 9.5 - - - +
74B ASN* 3.1 48.0 + - - +
75B GLN* 2.8 37.0 + - - +
76B THR* 3.7 28.3 - - - +
122B LEU* 4.2 8.3 - - - +
136B GLU* 2.8 41.2 + - - +
26C ASP* 4.3 3.3 - - - +
111C VAL* 3.8 20.9 - - + +
112C TYR 3.2 3.6 - - - -
113C ARG* 3.8 22.0 - - + +
123C TYR* 4.9 1.1 - - - -
124C LYS* 1.3 73.6 - - - +
126C ILE* 1.3 66.7 + - - +
127C THR* 4.3 1.0 + - - +
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Residues in contact with ILE 126 (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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23C VAL* 3.9 11.7 - - + -
25C LYS 4.1 9.0 - - - +
26C ASP 3.7 4.0 - - - +
28C TYR* 3.6 32.5 - - + -
38C ILE* 4.2 12.8 - - + -
39C GLU 3.7 29.8 - - - +
40C CYS* 3.8 17.7 - - - -
57C TRP* 3.9 17.0 - - + -
110C GLY 3.7 0.5 - - - +
111C VAL* 3.3 2.2 - - - -
112C TYR* 2.5 53.8 + - + +
124C LYS 5.1 1.1 - - - +
125C ARG* 1.3 80.4 - - - +
127C THR* 1.3 67.3 + - - +
128C VAL* 3.7 2.4 + - + -
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Residues in contact with THR 127 (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 ASP 2.8 16.6 + - - -
27C LEU* 3.3 23.0 - - + +
28C TYR 2.8 26.7 + - - +
110C GLY 3.4 8.5 - - - +
111C VAL* 4.0 18.8 - - + +
125C ARG* 4.2 0.9 - - - +
126C ILE* 1.3 74.8 - - - +
128C VAL* 1.3 69.4 + - - +
129C LYS* 3.8 16.2 - - + +
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Residues in contact with VAL 128 (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 TYR* 3.5 7.4 - - + +
30C VAL* 4.2 5.8 - - + -
36C MET* 3.7 31.4 - - + -
38C ILE* 4.3 15.0 - - + -
108C ASP 3.6 15.3 - - - +
109C ALA* 3.2 5.9 - - - +
110C GLY 2.6 34.9 + - - +
112C TYR* 3.5 32.8 - - + -
126C ILE* 4.5 3.8 - - + -
127C THR* 1.3 79.5 - - - +
129C LYS* 1.3 63.1 + - - +
130C VAL* 4.0 16.8 - - + -
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Residues in contact with LYS 129 (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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27C LEU* 3.9 17.1 - - + +
28C TYR 2.7 15.0 + - - +
29C VAL* 3.1 20.0 - - + -
30C VAL* 2.9 26.9 + - - +
109C ALA* 4.5 2.5 - - + -
127C THR* 3.8 22.2 - - - +
128C VAL* 1.3 75.0 - - - +
130C VAL* 1.3 62.8 + - - +
131C ASN* 5.8 1.3 - - - +
215C ASP* 6.4 2.2 - - + -
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Residues in contact with VAL 130 (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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30C VAL* 3.4 16.8 - - + +
32C TYR* 4.0 17.5 - - + -
104C VAL* 3.8 30.1 - - + -
105C LYS 4.3 12.1 - - - +
106C LEU* 4.7 11.0 - - + +
109C ALA* 4.0 28.4 - - + +
128C VAL* 4.0 7.0 - - + -
129C LYS* 1.3 77.2 - - - +
131C ASN* 1.3 73.3 + - - +
160C TYR* 3.7 24.6 - - - -
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Residues in contact with ASN 131 (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 VAL* 3.4 20.9 - - - +
30C VAL 3.0 9.4 + - - +
31C GLU* 3.7 7.3 - - + -
32C TYR* 2.7 35.9 + - - +
106C LEU* 6.1 0.2 - - - -
129C LYS* 5.5 1.4 - - - +
130C VAL* 1.3 79.3 + - - +
132C ALA* 1.3 58.0 + - - +
133C PRO* 4.5 0.9 - - + -
160C TYR* 3.8 6.5 + - - -
161C PRO* 4.8 2.4 - - - +
213C ARG* 3.9 15.6 + - - +
215C ASP* 2.7 25.9 + - - +
216C PRO* 3.3 21.1 - - - +
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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