Contacts of the strand formed by residues 19 - 26 (chain T) in PDB entry 2P8Z
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 VAL 19 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12T LEU 4.3 13.0 - - - +
13T MET* 4.9 3.6 - - - -
15T LYS 3.8 3.4 - - - +
16T VAL* 3.7 32.8 - - + +
17T THR 3.4 1.6 - - - -
18T ASN* 1.3 82.0 - - - +
20T ARG* 1.3 81.4 + - - +
21T ASN* 3.6 29.2 - - - +
99T LEU* 3.2 23.6 - - + +
101T ASN* 3.9 7.4 - - - +
344T SER* 3.2 15.9 - - - -
345T PRO* 4.8 6.1 - - + -
451T GLY 5.6 2.0 - - - +
452T ASN* 5.4 5.6 - - - +
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Residues in contact with ARG 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T THR 3.3 20.6 + - - -
18T ASN* 3.9 5.7 - - - +
19T VAL* 1.3 94.4 + - - +
21T ASN* 1.3 65.2 + - - +
22T MET* 3.7 3.7 + - + -
89T ILE* 4.1 7.7 - - - +
91T GLN* 3.9 17.6 - - - +
93T THR* 5.3 1.0 + - - -
98T PHE* 4.1 19.1 - - + -
99T LEU 2.9 8.5 + - - +
100T ILE* 3.5 21.0 - - + +
101T ASN 2.8 29.1 + - - +
338T ILE* 3.4 25.4 + - + +
339T VAL* 2.7 33.3 + - + +
342T LEU* 3.0 28.4 + - + -
343T PRO 3.6 11.4 - - - -
344T SER* 3.6 5.1 - - - -
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Residues in contact with ASN 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T VAL* 3.6 11.4 - - - +
20T ARG* 1.3 71.5 - - - +
22T MET* 1.3 59.1 + - - +
101T ASN* 2.8 36.1 + - - +
103T ILE* 4.6 3.1 - - + -
121T VAL 3.8 18.6 - - - +
122T THR* 4.1 2.7 - - - -
123T ASP* 2.9 39.9 + - - +
124T GLY 3.2 7.3 + - - -
342T LEU* 6.0 0.2 - - - +
343T PRO 4.7 3.3 + - - +
344T SER* 5.8 0.6 - - - +
345T PRO* 3.6 26.7 - - - +
399T ARG* 4.6 2.9 + - - -
451T GLY 4.0 6.7 + - - +
452T ASN* 6.2 0.2 - - - +
453T ILE* 4.2 17.3 - - - +
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Residues in contact with MET 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ARG* 4.3 3.1 - - + +
21T ASN* 1.3 74.6 - - - +
23T SER* 1.3 71.3 + - - +
24T VAL* 4.6 0.9 - - + -
100T ILE* 4.2 18.4 - - + -
101T ASN 3.0 12.5 + - - +
102T LEU* 3.1 37.0 - - + -
103T ILE* 2.8 34.5 + - - +
122T THR* 3.9 9.0 - - - +
124T GLY* 3.0 24.0 - - - +
126T LEU* 3.8 20.0 - - + +
338T ILE* 3.8 26.7 - - + -
342T LEU* 3.9 14.8 - - + -
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Residues in contact with SER 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22T MET* 1.3 82.8 - - - +
24T VAL* 1.3 69.0 + - - +
25T ILE* 4.1 1.6 - - - +
102T LEU* 4.9 1.3 - - - -
103T ILE* 3.2 24.5 - - - +
105T SER* 4.8 9.9 + - - -
118T ALA 6.4 0.2 - - - -
119T LEU* 3.8 22.9 - - - +
122T THR* 4.2 12.6 + - - +
124T GLY 3.4 3.0 + - - -
125T ALA* 3.5 9.4 - - - +
126T LEU 2.9 24.8 + - - -
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Residues in contact with VAL 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T SER* 1.3 79.8 + - - +
25T ILE* 1.3 64.3 + - - +
32T LYS* 3.3 50.8 + - + +
35T LEU* 5.4 2.5 - - + -
36T THR* 4.0 17.3 - - + -
39T LEU* 5.4 1.8 - - + -
102T LEU* 3.9 24.0 - - + -
103T ILE 4.6 1.4 + - - -
105T SER* 3.7 7.3 + - - -
126T LEU* 3.3 30.3 - - + +
128T VAL* 3.5 24.7 - - + -
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Residues in contact with ILE 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T SER* 4.5 6.3 - - - +
24T VAL* 1.3 74.5 - - - +
26T ALA* 1.3 66.9 + - - +
32T LYS* 5.1 0.4 - - - +
119T LEU* 4.7 3.4 - - + -
125T ALA* 3.9 22.9 - - + -
126T LEU 2.9 8.6 + - - +
127T VAL* 3.5 20.9 - - + +
128T VAL 2.8 29.5 + - - +
139T THR* 4.2 11.2 - - + +
142T VAL* 3.5 45.8 - - + +
143T LEU* 4.0 13.0 - - + +
146T ALA* 3.8 25.4 - - + -
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Residues in contact with ALA 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T VAL 4.0 1.8 + - - -
25T ILE* 1.3 82.9 - - - +
27T HIS* 1.3 68.4 + - - +
28T VAL* 3.8 0.7 + - - -
30T HIS* 4.5 2.9 - - + -
32T LYS* 3.6 41.4 + - + +
109T VAL* 6.1 0.9 - - - +
128T VAL* 3.6 25.8 - - + +
138T GLN* 4.5 2.6 - - - +
139T THR* 4.9 3.6 - - - -
142T VAL* 5.7 4.9 - - - +
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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