Contacts of the strand formed by residues 130 - 142 (chain C) in PDB entry 3RT0
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 LYS 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C HIS* 4.9 3.5 + - - -
36C LYS* 6.1 10.8 - - + -
125C GLU 4.1 0.2 - - - +
126C THR* 3.8 2.9 - - - -
127C ILE 3.1 28.8 + - - +
128C ASP* 3.6 14.4 - - + +
129C GLY* 1.3 83.1 - - - +
131C THR* 1.3 66.7 + - - +
132C GLY* 3.5 2.1 + - - -
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Residues in contact with THR 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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36C LYS* 4.9 2.1 - - - -
37C ALA* 4.3 10.1 + - - -
38C PRO* 4.4 10.3 - - + +
124C SER* 4.1 19.3 - - - +
125C GLU 4.9 0.4 - - - +
126C THR* 3.4 27.1 + - - +
129C GLY 4.0 2.0 + - - -
130C LYS* 1.3 73.9 - - - +
132C GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 132 (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 HIS* 4.1 5.4 - - - -
35C ILE 3.4 9.0 - - - -
36C LYS* 4.5 1.3 - - - -
37C ALA 3.2 14.8 - - - -
38C PRO* 4.5 0.7 - - - -
39C LEU 4.7 2.9 + - - -
124C SER* 3.8 8.5 + - - -
125C GLU 3.0 31.7 + - - -
130C LYS 3.5 1.2 + - - -
131C THR* 1.3 77.6 - - - +
133C THR* 1.3 65.9 + - - -
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Residues in contact with THR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS 3.8 0.2 - - - +
34C HIS* 3.5 8.9 + - - -
35C ILE* 2.7 42.2 + - + +
37C ALA 2.6 22.4 + - - -
38C PRO 3.4 0.2 - - - -
39C LEU* 3.1 30.4 + - + -
42C VAL* 3.5 21.2 - - + +
122C LEU* 4.0 25.4 - - + -
123C HIS 3.4 10.3 - - - +
125C GLU* 4.4 0.7 - - - +
132C GLY* 1.3 72.2 + - - -
134C LEU* 1.3 65.7 + - - +
135C ALA 4.6 0.4 - - - +
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Residues in contact with LEU 134 (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* 3.2 34.3 - - + -
33C LYS 3.4 14.1 - - - +
34C HIS* 4.1 3.6 - - + +
122C LEU* 3.6 1.9 - - - -
123C HIS* 2.7 47.5 + - + +
125C GLU* 3.5 35.5 - - + +
133C THR* 1.3 73.2 - - - +
135C ALA* 1.3 60.0 + - - +
136C ILE* 4.0 22.9 - - + -
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU 3.9 0.3 - - - +
32C VAL* 3.3 5.4 - - - +
33C LYS* 2.8 42.1 + - + +
35C ILE* 3.9 18.2 - - + -
120C ILE* 4.3 4.9 - - + -
121C SER 3.6 4.0 - - - -
122C LEU* 3.8 19.1 - - + -
133C THR* 3.9 1.8 + - + -
134C LEU* 1.3 72.7 - - - +
136C ILE* 1.3 62.2 + - - +
137C GLU 4.2 0.4 + - - -
164C LEU* 4.3 21.5 - - + +
167C LEU* 4.7 1.1 - - + -
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Residues in contact with ILE 136 (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 THR* 3.9 19.3 - - + -
31C LEU 3.4 8.7 - - - +
32C VAL* 3.6 19.5 - - + -
119C THR 3.6 0.9 - - - +
120C ILE* 3.2 4.6 - - - +
121C SER* 2.8 45.1 + - - +
123C HIS* 3.4 31.0 - - + +
134C LEU* 4.0 18.8 - - + -
135C ALA* 1.3 78.1 - - - +
137C GLU* 1.3 65.1 + - - +
138C SER* 5.1 1.8 - - - +
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Residues in contact with GLU 137 (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 THR* 3.5 2.3 - - - -
31C LEU* 2.7 43.6 + - - +
55C TYR* 5.4 2.6 + - - -
56C LYS* 5.3 7.1 + - - -
116C TYR* 4.7 1.7 + - - -
118C SER* 4.0 14.8 + - - -
119C THR 3.2 10.5 - - - +
120C ILE* 3.8 20.0 - - + +
135C ALA 4.2 0.4 - - - -
136C ILE* 1.3 76.1 - - - +
138C SER* 1.3 67.6 + - - +
160C ILE* 3.9 40.3 - - + +
163C ASN* 5.2 8.8 + - - +
164C LEU* 3.8 22.4 - - + +
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Residues in contact with SER 138 (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 SER* 5.6 1.1 - - - -
29C SER 3.3 14.4 - - - -
30C THR* 3.5 16.6 - - - -
118C SER* 3.2 5.9 - - - -
119C THR* 2.9 43.8 + - - +
136C ILE* 5.1 2.2 - - - +
137C GLU* 1.3 77.1 - - - +
139C PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 139 (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 CYS* 4.5 0.4 - - - -
28C SER* 2.8 31.5 + - - -
29C SER* 3.2 43.4 + - - -
31C LEU* 4.5 1.8 - - + -
116C TYR* 3.6 26.9 - + + +
117C SER 3.3 11.4 - - - +
118C SER* 3.9 1.1 - - - +
138C SER* 1.3 78.2 - - - +
140C VAL* 1.3 68.0 + - - +
141C VAL* 4.1 13.7 - - + -
153C CYS* 4.1 17.7 - - - -
156C VAL* 3.6 41.5 - - + -
157C GLU* 4.3 7.9 - - + -
160C ILE* 3.5 20.6 - - + -
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Residues in contact with VAL 140 (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 GLN* 3.5 28.9 - - + +
27C CYS 3.5 7.2 - - - +
28C SER* 3.5 18.8 - - - +
115C ASN 3.3 3.1 - - - +
116C TYR* 3.3 3.3 - - - +
117C SER* 2.9 41.2 + - - +
139C PHE* 1.3 80.9 - - - +
141C VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 141 (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 GLN* 3.0 12.7 - - - -
27C CYS* 2.8 40.2 + - - -
113C LEU* 3.8 19.5 - - + -
114C LYS 3.2 23.6 - - - +
115C ASN 3.9 2.2 - - - -
116C TYR* 3.8 19.3 - - + -
139C PHE* 4.1 12.8 - - + -
140C VAL* 1.3 77.2 - - - +
142C ASP* 1.3 74.5 + - - +
152C THR* 3.8 28.3 - - + -
156C VAL* 4.7 0.7 - - + -
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Residues in contact with ASP 142 (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 GLU* 3.6 27.9 - - - +
25C SER 3.2 7.2 - - - +
26C GLN* 2.3 43.3 - - - +
112C ARG 4.4 1.9 - - - +
114C LYS* 2.9 38.4 + - + +
115C ASN* 3.1 24.0 + - - +
141C VAL* 1.3 83.5 - - - +
143C VAL* 1.3 64.3 + - - +
144C PRO* 3.3 9.1 - - + +
152C THR* 4.6 0.3 - - - +
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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