Contacts of the strand formed by residues 21 - 29 (chain A) in PDB entry 2VBJ
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 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE 3.7 2.4 + - - -
17A VAL* 2.9 26.5 + - - -
20A ASP* 1.3 80.6 - - - +
22A SER* 1.3 63.6 + - - -
44A LYS 3.2 12.1 - - - -
45A VAL* 4.1 7.6 - - - -
98A LYS* 3.2 20.8 + - - -
15C A 3.5 10.7 - - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 5.0 2.6 - - - +
21A GLY* 1.3 75.2 - - - -
23A ILE* 1.3 64.4 + - - +
24A ILE* 3.2 27.5 - - - +
42A THR 3.7 1.6 - - - +
43A PHE* 3.6 3.3 - - - -
44A LYS* 2.8 42.2 + - - +
46A THR* 6.0 0.4 - - - -
98A LYS* 4.2 2.0 - - - +
136A ASN* 4.9 0.3 + - - -
15C A 3.5 19.0 - - - +
16C G 2.9 24.5 + - - +
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Residues in contact with ILE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 5.0 4.9 - - + -
22A SER* 1.3 77.4 + - - +
24A ILE* 1.3 60.0 + - - +
42A THR 3.7 5.8 - - - +
43A PHE* 4.1 16.8 - - + -
88A LEU* 4.0 18.8 - - + -
95A LEU* 4.2 8.3 - - + -
98A LYS* 3.9 21.8 - - + +
101A GLN* 4.0 18.2 - - + +
102A ALA* 3.9 29.4 - - + +
105A VAL* 3.4 33.0 - - + -
132A ILE* 3.6 7.5 - - + +
136A ASN* 3.0 24.3 + - - +
16C G 4.5 1.6 + - - -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A SER* 3.2 22.9 - - - +
23A ILE* 1.3 73.6 - - - +
25A ALA* 1.3 61.8 + - - +
26A GLN* 3.8 27.6 - - + +
40A LYS 3.8 0.3 - - - +
41A LEU* 3.4 4.9 - - - +
42A THR* 2.8 51.3 + - + +
44A LYS* 4.1 21.8 - - + +
105A VAL* 5.1 2.5 - - - +
132A ILE* 4.9 0.2 - - - -
136A ASN* 4.5 2.9 - - - +
16C G 3.6 36.1 - - + +
17C G 3.7 30.7 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE 4.3 1.0 + - - -
24A ILE* 1.3 77.3 - - - +
26A GLN* 1.3 64.2 + - - +
40A LYS 3.5 4.3 - - - -
41A LEU* 3.9 15.0 - - + -
105A VAL* 5.1 0.2 - - + -
129A VAL* 3.4 28.1 - - + +
132A ILE* 3.5 38.6 - - + +
133A ALA* 5.3 1.2 + - - +
136A ASN* 5.3 0.4 - - - +
141A ARG* 3.5 9.9 + - - -
17C G 4.3 7.0 + - - +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.8 17.2 - - + +
25A ALA* 1.3 77.8 - - - +
27A ILE* 1.3 67.1 + - - +
28A GLU* 4.0 1.3 - - + +
39A LEU* 3.4 6.8 - - - +
40A LYS* 2.8 54.0 + - + +
41A LEU* 4.7 0.4 - - - +
42A THR* 4.6 8.5 + - - -
129A VAL* 4.0 3.9 - - - +
141A ARG* 4.5 2.5 - - - +
17C G 3.6 24.0 - - - +
18C A 2.8 63.3 + - - +
19C T 4.1 9.4 - - + +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 1.3 77.4 - - - +
28A GLU* 1.3 58.9 + - - +
29A PRO* 3.8 0.7 - - - +
37A HIS* 3.8 16.6 - - + -
38A ARG 3.5 4.9 - - - +
39A LEU* 3.8 17.0 - - + -
126A CYS* 3.9 25.1 - - + +
129A VAL* 3.9 7.2 - - + +
141A ARG* 3.9 18.1 - - - +
143A THR* 3.4 35.6 + - + +
144A THR* 3.7 6.7 - - - +
145A SER 3.7 26.5 - - - +
148A VAL* 3.5 24.9 - - + -
18C A 4.6 6.3 + - - -
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 4.0 1.3 - - + -
27A ILE* 1.3 73.1 - - - +
29A PRO* 1.3 82.3 - - + +
30A ASN* 3.5 10.6 + - - -
37A HIS* 3.1 5.4 - - - -
38A ARG* 2.8 67.7 + - - +
40A LYS* 3.3 10.0 + - + -
19C T 3.8 25.5 - - + +
20C C 2.8 47.6 + - - -
21C C 5.6 0.2 - - - -
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Residues in contact with PRO 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 3.8 6.7 - - - +
28A GLU* 1.3 98.9 - - + +
30A ASN* 1.3 63.6 + - - +
36A LYS 3.5 7.6 - - - +
37A HIS* 3.7 14.7 - - + +
143A THR* 3.7 21.1 - - + +
147A THR* 6.0 2.0 - - + -
18C A 6.1 0.9 - - + -
19C T 4.2 19.3 - - + +
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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