Contacts of the strand formed by residues 34 - 43 (chain C) in PDB entry 1TJJ
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 ASN 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PRO* 3.6 14.6 - - - +
30C VAL* 4.9 3.3 - - - +
33C GLY* 1.3 76.8 - - - +
35C VAL* 1.3 68.0 + - - +
36C THR* 5.9 0.4 - - + -
122C GLU* 3.3 35.8 + - + +
123C PHE 3.1 14.8 - - - +
124C VAL* 3.5 23.0 - - - +
125C VAL* 4.8 0.2 - - - +
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Residues in contact with VAL 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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24C LEU* 4.1 15.3 - - + -
25C GLU 3.1 13.2 - - - +
26C PRO* 4.3 1.3 - - + -
29C ILE* 3.4 41.3 - - + -
34C ASN* 1.3 75.7 - - - +
36C THR* 1.3 64.8 + - - +
37C LEU* 5.3 1.1 - - + +
121C SER 3.8 0.5 - - - +
122C GLU* 3.4 2.7 - - - -
123C PHE* 2.8 51.2 + - + +
125C VAL* 3.5 11.4 - - + -
1514C IPA 4.0 24.2 - - + -
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Residues in contact with THR 36 (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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81A HIS* 4.3 24.5 - - + +
23C THR* 3.8 2.0 + - - +
24C LEU* 3.5 4.4 + - - -
25C GLU* 2.7 67.2 + - - +
26C PRO* 6.3 0.2 - - + -
34C ASN* 5.9 0.4 - - + -
35C VAL* 1.3 76.5 - - - +
37C LEU* 1.3 60.4 + - - +
120C LYS* 5.3 4.7 - - - -
121C SER 3.4 6.7 - - - +
122C GLU* 4.3 22.9 - - + +
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Residues in contact with LEU 37 (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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22C LEU* 3.7 30.1 - - + -
23C THR* 3.4 9.6 - - - +
24C LEU* 4.2 18.2 - - + -
35C VAL* 4.0 1.7 - - + -
36C THR* 1.3 74.3 - - - +
38C SER* 1.3 64.6 + - - +
39C VAL* 4.8 2.5 - - + -
118C LEU* 4.0 11.6 - - + +
119C PRO 3.9 1.7 - - - +
120C LYS* 3.4 2.2 - - - -
121C SER* 2.9 32.5 + - - +
123C PHE* 3.7 31.6 - - + -
1513C IPA 4.0 23.3 - - + +
1514C IPA 6.0 5.6 - - + -
2486C PFS 3.7 19.5 - - + -
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Residues in contact with SER 38 (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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84A ASP* 3.7 7.0 + - - -
88A MET* 3.8 8.9 - - - +
21C SER* 5.5 1.2 + - - -
22C LEU* 3.4 5.5 + - - +
23C THR* 2.5 57.8 + - - +
37C LEU* 1.3 75.1 - - - +
39C VAL* 1.3 66.3 + - - +
118C LEU* 3.2 16.6 - - - -
120C LYS* 3.5 24.6 - - - +
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Residues in contact with VAL 39 (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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88A MET* 4.3 0.4 - - - +
19C ILE* 4.1 18.6 - - + -
21C SER* 3.3 15.5 - - - +
22C LEU* 3.9 16.4 - - + -
37C LEU* 4.8 3.1 - - + -
38C SER* 1.3 79.0 - - - +
40C VAL* 1.3 72.1 + - - +
116C TYR 3.9 1.2 - - - +
117C SER* 3.7 0.5 - - - -
118C LEU* 2.8 48.6 + - + +
1513C IPA 4.4 7.9 - - - +
2486C PFS 3.3 41.4 - - + +
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Residues in contact with VAL 40 (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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88A MET* 3.8 24.7 - - + -
19C ILE* 3.7 3.8 - - - +
20C ARG* 2.7 37.1 + - + -
21C SER* 2.9 32.6 + - - +
39C VAL* 1.3 81.4 - - - +
41C GLY* 1.3 61.4 + - - +
115C THR* 3.8 25.6 - - + -
116C TYR 3.3 5.4 - - - +
117C SER* 3.8 16.2 - - - +
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Residues in contact with GLY 41 (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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18C VAL 3.4 10.8 - - - -
19C ILE* 4.2 6.5 - - - -
20C ARG* 4.2 2.5 - - - -
40C VAL* 1.3 77.4 - - - +
42C SER* 1.3 61.7 + - - -
115C THR* 3.4 3.5 - - - +
116C TYR* 2.7 39.6 + - - +
2486C PFS 4.2 4.6 - - - +
2488C LPE 3.8 17.0 - - - -
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Residues in contact with SER 42 (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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16C PRO 3.6 2.0 + - - +
17C ALA* 3.3 1.4 - - - -
18C VAL* 2.8 34.6 + - - +
20C ARG* 3.3 34.4 + - - +
41C GLY* 1.3 74.2 - - - -
43C THR* 1.3 62.6 + - - +
114C GLY 3.2 8.5 - - - -
115C THR* 3.3 26.0 - - - -
2488C LPE 3.8 5.5 - - - +
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Residues in contact with THR 43 (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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16C PRO 3.2 4.4 + - - -
17C ALA* 3.8 15.7 - - - +
42C SER* 1.3 77.6 - - - +
44C SER* 1.3 59.8 + - - +
45C VAL* 2.7 34.8 + - - +
47C LEU* 3.6 23.6 - - + +
111C PHE 4.8 0.4 - - - +
112C LYS 3.9 20.0 - - - +
113C GLU* 3.3 4.4 - - - +
114C GLY* 2.9 30.5 + - - +
116C TYR* 4.5 2.0 - - + -
2488C LPE 4.2 11.7 - - + -
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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