Contacts of the strand formed by residues 33 - 43 (chain B) 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 GLY 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.6 10.9 + - - -
31B VAL* 4.0 0.2 - - - +
32B PRO* 1.3 77.3 - - - +
34B ASN* 1.3 69.4 + - - +
124B VAL* 4.0 2.6 - - - +
125B VAL* 2.9 29.8 + - - +
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PRO* 3.7 15.1 - - - +
29B ILE* 5.1 0.3 - - - +
30B VAL 4.8 3.5 + - - +
33B GLY* 1.3 77.8 - - - -
35B VAL* 1.3 71.5 + - - +
122B GLU* 4.7 12.6 - - + +
123B PHE 3.2 12.1 - - - +
124B VAL* 3.3 32.3 - - - +
125B VAL* 4.5 0.2 - - - +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.2 11.4 - - + -
25B GLU 3.2 11.9 - - - +
26B PRO* 4.4 1.3 - - + -
29B ILE* 3.3 44.2 - - + -
34B ASN* 1.3 75.8 - - - +
36B THR* 1.3 61.6 + - - +
37B LEU* 4.1 0.6 + - + -
121B SER 3.7 0.5 - - - +
122B GLU* 3.4 5.1 - - - +
123B PHE* 2.9 50.2 + - + +
124B VAL 5.5 0.2 - - - -
125B VAL* 3.4 13.7 - - + -
1364B DAO 3.9 28.5 - - + -
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Residues in contact with THR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.7 1.4 + - - +
24B LEU* 3.4 5.4 + - - +
25B GLU* 2.8 58.9 + - - +
35B VAL* 1.3 72.3 - - - +
37B LEU* 1.3 62.1 + - - +
120B LYS* 3.7 30.7 - - + -
121B SER 3.3 7.9 - - - +
122B GLU* 2.5 33.9 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.4 4.0 - - + -
23B THR* 3.2 11.4 - - - +
24B LEU* 4.0 17.3 - - + -
35B VAL* 4.1 1.5 - - + -
36B THR* 1.3 75.3 - - - +
38B SER* 1.3 77.8 + - - +
39B VAL* 3.9 18.6 - - + -
118B LEU* 4.0 12.8 - - + +
119B PRO 3.6 2.6 - - - +
120B LYS* 3.4 2.4 - - - -
121B SER* 2.9 31.6 + - - +
123B PHE* 4.2 13.0 - - + -
1364B DAO 4.1 15.5 - - + -
2484B PFS 3.5 36.1 - - + -
2485B LPE 4.2 10.1 - - + -
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 5.4 3.3 + - - -
22B LEU* 3.4 6.6 + - - +
23B THR* 2.5 52.9 + - - +
37B LEU* 1.3 76.0 - - - +
39B VAL* 1.3 65.6 + - - +
118B LEU 3.3 14.1 - - - -
119B PRO* 3.9 0.9 - - - -
120B LYS* 3.5 24.8 - - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.1 16.6 - - + -
21B SER* 3.3 14.4 - - - +
22B LEU* 3.8 17.7 - - + -
37B LEU* 3.9 9.2 - - + -
38B SER* 1.3 79.1 - - - +
40B VAL* 1.3 69.7 + - - +
118B LEU* 2.8 37.7 + - + +
2484B PFS 3.5 43.2 - - + +
2485B LPE 3.9 18.8 - - + -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.6 4.0 - - - +
20B ARG* 2.7 45.3 + - + -
21B SER* 2.9 31.9 + - - +
39B VAL* 1.3 83.7 - - - +
41B GLY* 1.3 57.3 + - - +
115B THR* 3.9 15.5 - - + -
116B TYR 3.3 4.7 - - - +
117B SER* 3.7 28.7 - - - +
118B LEU 4.8 1.8 - - - +
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL 3.3 11.4 - - - -
19B ILE* 4.2 2.5 - - - -
20B ARG* 4.2 1.3 - - - -
40B VAL* 1.3 76.2 - - - +
42B SER* 1.3 59.0 + - - -
115B THR* 3.4 4.2 - - - +
116B TYR* 2.7 35.8 + - - +
2484B PFS 3.7 10.1 - - - +
2485B LPE 3.9 18.4 - - - -
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 3.7 1.5 + - - +
17B ALA* 3.3 2.1 - - - -
18B VAL* 2.9 38.3 + - - +
20B ARG* 3.0 39.9 + - - +
41B GLY* 1.3 73.1 - - - -
43B THR* 1.3 62.4 - - - +
114B GLY 3.2 8.1 - - - -
115B THR* 3.4 22.4 - - - -
2485B LPE 3.8 5.8 - - - +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 3.2 9.1 + - - -
17B ALA* 3.8 13.2 - - - +
42B SER* 1.3 79.2 - - - +
44B SER* 1.3 61.5 + - - +
45B VAL* 2.7 32.0 + - - +
47B LEU* 3.8 24.5 - - + +
111B PHE* 4.8 0.9 - - + +
112B LYS 3.9 19.5 - - - +
113B GLU* 3.3 3.7 - - - +
114B GLY* 3.0 31.9 + - - +
116B TYR* 4.6 4.3 - - + -
2485B LPE 4.1 8.1 - - + -
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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