Contacts of the strand formed by residues 20 - 28 (chain A) in PDB entry 2F24
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 TYR 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.9 29.6 - + + +
14A GLN 3.3 37.9 - - - -
15A SER* 3.6 12.2 - - - +
18A HIS 3.3 0.8 - - - +
19A ALA* 1.3 83.3 - - + +
21A ARG* 1.3 69.6 + - - +
38A ALA* 4.8 1.1 - - + -
39A GLU 3.3 11.4 - - - +
40A GLN* 2.9 44.2 + - + -
53A VAL* 4.0 7.9 - - + -
71A GLN* 3.1 28.3 + - - -
355A GLU* 5.5 0.9 - - - +
359A TYR* 3.9 13.2 - - - +
360A GLU 5.6 0.6 - - - -
361A GLU* 5.0 3.6 + - - +
362A ILE* 3.9 15.7 - - + +
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Residues in contact with ARG 21 (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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18A HIS* 4.7 9.9 - - - +
19A ALA 4.1 1.0 + - - -
20A TYR* 1.3 82.1 - - - +
22A ILE* 1.3 82.8 + - + +
23A PRO* 3.7 1.6 - - - -
38A ALA* 3.7 1.9 - - - -
39A GLU* 2.8 36.7 + - + +
41A ARG* 6.3 0.2 - - - -
304A ARG* 4.1 5.9 - - - +
334A TYR* 3.3 32.3 + - - -
355A GLU* 2.7 38.7 + - + +
359A TYR* 3.4 39.6 - - + -
362A ILE* 3.9 6.7 - - - +
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Residues in contact with ILE 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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21A ARG* 1.3 96.1 - - + +
23A PRO* 1.3 68.6 - - - +
38A ALA* 3.7 3.9 - - - -
39A GLU* 3.3 35.7 - - - +
86A ASN* 4.2 6.3 - - - +
87A PRO* 3.6 22.0 - - + +
161A PRO* 3.3 33.9 - - + -
334A TYR* 3.8 27.1 - - + -
355A GLU* 2.7 19.0 + - - +
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Residues in contact with PRO 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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21A ARG 3.7 1.7 - - - -
22A ILE* 1.3 89.8 - - - +
24A ALA* 1.3 60.5 + - - +
37A PHE 3.5 7.2 - - - +
38A ALA* 4.6 1.3 - - - -
161A PRO* 4.6 4.9 - - - +
162A GLY* 4.1 9.5 + - - -
273A GLN* 5.6 0.5 + - - -
334A TYR* 3.9 23.8 - - + +
335A SER* 4.2 4.3 - - - +
336A ASP* 3.9 10.1 - - - +
353A LEU* 3.7 43.1 - - + +
354A TYR* 4.3 0.7 - - - -
355A GLU* 3.6 20.4 - - + +
362A ILE* 4.0 12.6 - - + -
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Residues in contact with ALA 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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23A PRO* 1.3 76.2 - - - +
25A LEU* 1.3 60.0 + - - +
35A LEU 3.7 1.0 - - - +
36A ALA* 3.6 0.2 - - - -
37A PHE* 2.8 40.9 + - + +
87A PRO* 3.4 36.3 - - + +
89A PRO* 3.5 18.8 - - + -
162A GLY* 3.9 3.6 - - - -
336A ASP* 3.4 7.4 - - - -
353A LEU* 3.5 5.0 - - - +
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Residues in contact with LEU 25 (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 ALA* 1.3 75.3 - - - +
26A LEU* 1.3 61.6 + - - +
34A LEU* 4.0 28.7 - - + -
35A LEU 3.5 12.3 - - - +
36A ALA* 4.3 11.7 - - + -
68A TRP* 4.3 6.7 - - + -
89A PRO* 4.1 2.9 - - - +
163A HIS* 3.6 8.5 - - - +
336A ASP* 2.7 33.3 + - - +
338A GLN* 3.1 34.1 - - + +
351A GLY* 3.4 38.8 - - - +
352A CYS* 3.9 4.3 - - - +
353A LEU* 4.3 13.2 - - + +
364A PHE* 4.3 6.1 - - + -
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Residues in contact with LEU 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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25A LEU* 1.3 78.0 - - - +
27A TYR* 1.3 65.4 + - - +
28A LEU* 4.0 18.5 + - + +
33A SER 3.9 0.2 - - - +
34A LEU* 3.3 8.1 - - - -
35A LEU* 2.9 50.8 + - + +
37A PHE* 5.0 0.4 - - + -
89A PRO* 3.9 28.3 - - + +
90A LEU* 3.9 26.5 - - + +
91A TYR* 3.8 23.8 - - + +
98A LEU* 4.2 14.8 - - + -
99A PHE 5.1 0.4 - - - +
136A TRP* 6.1 0.9 - - + -
163A HIS* 5.1 2.0 - - + -
338A GLN* 3.5 14.1 - - - +
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Residues in contact with TYR 27 (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 LEU* 1.3 78.6 - - - +
28A LEU* 1.3 72.3 + - - +
29A PRO* 3.5 35.9 + - + +
32A GLN* 3.5 34.2 + - - +
33A SER 3.4 18.8 - - - -
34A LEU* 3.7 19.3 - - + -
59A TYR* 5.5 3.9 - - + +
91A TYR* 4.2 7.6 - - - +
338A GLN* 2.9 19.7 + - + +
339A SER 3.4 23.8 - - - +
340A MET* 3.5 46.3 + - + -
341A GLY* 4.3 3.1 - - - -
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Residues in contact with LEU 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 LEU* 4.0 11.9 - - + +
27A TYR* 1.3 80.0 - - - +
29A PRO* 1.3 59.4 - - - +
30A GLY 3.4 1.3 - - - -
31A GLN* 4.2 11.9 - - + -
32A GLN* 2.7 36.0 + - - -
33A SER* 2.9 20.0 + - - +
35A LEU* 4.3 12.8 - - + -
56A ARG* 4.2 9.6 - - - +
91A TYR* 4.3 4.7 - - + -
98A LEU* 3.4 38.4 - - + -
132A HIS* 3.6 37.2 - - + +
1001A CL 3.6 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