Contacts of the strand formed by residues 16 - 23 (chain B) in PDB entry 4HXG
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 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 2.9 36.3 + - - +
14B PHE* 3.4 42.1 - + + -
15B ALA* 1.3 75.2 - - - +
17B LEU* 1.3 63.0 + - - +
18B SER* 5.0 0.8 + - - -
30B VAL 3.3 2.6 - - - +
32B THR* 2.7 58.4 + - + +
33B LYS* 5.1 2.5 - - - -
34B ALA* 5.2 10.8 - - + -
41B TYR* 6.3 2.5 - + - -
322B PRO* 5.0 13.0 - - + -
396B PHE* 5.9 4.2 - + - -
398B TYR* 5.5 0.5 - - - -
589B ARG* 4.7 13.2 + - - -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ALA 3.9 6.9 + - - +
16B TYR* 1.3 82.3 - - - +
18B SER* 1.3 63.2 + - - +
29B TYR* 4.0 16.4 - - + -
30B VAL 3.2 3.1 - - - +
31B LEU* 3.7 29.4 - - + -
304B MET* 6.2 0.2 - - - +
315B LEU* 3.5 26.4 - - + +
323B ALA* 3.9 31.4 + - - +
324B GLU* 4.2 6.3 - - - +
325B LEU* 4.3 4.7 - - + +
336B THR* 3.9 12.1 - - - +
338B TYR* 3.5 37.5 - - + -
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR 5.0 0.6 + - - -
17B LEU* 1.3 77.2 - - - +
19B ASP* 1.3 71.8 + - - +
20B PRO* 3.5 3.7 - - - -
29B TYR* 3.7 2.4 - - - +
30B VAL* 2.9 49.4 + - - +
32B THR* 4.5 5.0 + - - -
315B LEU* 3.8 6.4 - - - +
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Residues in contact with ASP 19 (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 SER* 1.3 80.0 - - - +
20B PRO* 1.3 73.3 - - - +
21B ARG* 3.1 31.0 + - - +
28B ALA 3.8 4.7 - - - +
29B TYR* 3.8 3.8 - - - -
30B VAL* 4.1 10.1 - - + -
63B MET* 3.7 6.1 + - - +
64B PRO* 3.7 13.0 - - - +
65B ARG* 2.9 28.8 + - - -
315B LEU* 4.3 0.4 - - - +
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Residues in contact with PRO 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER 3.5 0.4 - - - -
19B ASP* 1.3 90.0 - - - +
21B ARG* 1.3 69.1 + - - +
28B ALA 3.4 7.0 - - - +
29B TYR* 4.2 5.2 - - + -
268B LYS* 4.3 2.4 + - - -
305B GLY* 3.8 16.4 - - - +
306B PHE* 3.7 28.9 - - - +
307B ASP* 3.7 8.4 - - - +
313B ILE* 3.6 21.8 - - + -
315B LEU* 3.9 24.7 - - + +
325B LEU* 4.4 5.8 - - + -
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Residues in contact with ARG 21 (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 ASP* 3.1 27.1 + - - +
20B PRO* 1.3 80.2 + - - +
22B THR* 1.3 65.4 + - - +
27B VAL* 3.4 5.4 - - - +
28B ALA* 2.7 41.9 + - + +
64B PRO* 3.5 20.9 - - + +
65B ARG* 3.0 50.8 - - - +
66B ILE* 4.6 11.7 - - + +
268B LYS* 4.4 14.5 - - - +
270B ARG* 6.0 3.4 - - - +
307B ASP* 3.3 14.2 + - - +
313B ILE* 4.0 1.9 - - - +
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Residues in contact with THR 22 (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 ARG* 1.3 77.0 - - - +
23B ARG* 1.3 77.4 + - - +
24B LYS 4.1 8.0 + - - -
26B LEU 2.9 19.2 + - - -
27B VAL* 4.1 4.8 - - - +
66B ILE* 4.3 4.0 - - - -
270B ARG* 5.4 1.0 + - - -
307B ASP* 2.8 53.7 + - + +
308B ALA* 3.6 3.5 - - - +
309B ASP* 3.7 18.9 + - - +
311B ARG* 4.0 11.6 + - - +
313B ILE* 3.9 12.8 - - + -
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Residues in contact with ARG 23 (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 THR* 1.3 89.2 + - - +
24B LYS* 1.3 72.0 + - + +
26B LEU* 2.9 24.3 + - + +
66B ILE* 3.4 49.9 + - + +
67B SER 3.8 9.4 - - - +
68B PRO* 3.8 26.7 - - - +
70B GLY* 4.7 6.7 - - - -
270B ARG* 5.4 7.7 - - - +
307B ASP* 5.4 0.9 - - - -
309B ASP* 3.7 21.0 - - - +
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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