Contacts of the strand formed by residues 40 - 48 (chain B) in PDB entry 5H9U
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 ARG 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B LYS* 3.1 29.0 + - - +
39B ALA* 1.3 72.2 - - - +
41B VAL* 1.3 59.8 + - - +
42B ALA 4.4 0.2 - - - -
57B GLU 4.1 0.7 - - - +
58B ILE* 3.4 4.5 - - - +
59B THR* 2.8 64.4 + - - +
102B PRO* 4.6 8.1 - - - +
106B GLY 3.9 18.8 + - - -
107B GLY* 4.2 3.4 - - - -
108B VAL* 3.4 40.6 - - - +
279B ASP* 3.2 12.8 - - - +
281B THR* 3.6 24.5 - - - +
282B LYS* 4.4 11.9 - - - +
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Residues in contact with VAL 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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28B ILE* 4.8 0.2 - - + -
29B LEU* 3.7 33.4 - - + +
32B LEU* 3.5 39.7 - - + -
39B ALA* 4.2 11.2 - - + +
40B ARG* 1.3 80.1 - - - +
42B ALA* 1.3 64.0 + - - +
43B ALA* 3.9 16.8 - - + +
57B GLU 3.9 2.0 - - - -
58B ILE* 4.4 6.1 - - + +
277B GLY 3.0 22.0 - - - +
278B LYS* 3.3 1.4 - - - -
279B ASP* 2.6 23.9 + - - -
282B LYS* 3.2 12.3 - - - -
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Residues in contact with ALA 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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41B VAL* 1.3 74.1 - - - +
43B ALA* 1.3 59.9 + - - +
44B GLU* 4.5 9.3 - - - +
56B GLY* 3.2 7.1 - - - -
57B GLU* 2.9 54.9 + - + +
58B ILE* 5.5 0.2 - - - -
277B GLY 3.2 4.5 - - - -
278B LYS* 4.9 7.9 - - + +
282B LYS* 4.2 18.4 - - + +
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Residues in contact with ALA 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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25B SER* 2.9 27.1 + - - +
28B ILE* 4.3 27.1 - - + -
41B VAL* 4.0 16.4 - - + -
42B ALA* 1.3 72.7 - - - +
44B GLU* 1.3 65.4 - - - +
54B VAL* 4.8 3.6 - - + -
55B ALA 3.7 5.8 - - - +
56B GLY* 4.7 0.4 - - - -
58B ILE* 5.3 5.6 - - + -
97B ILE* 6.2 1.1 - - + -
255B THR* 4.1 0.2 - - - +
276B SER 4.1 2.6 - - - +
277B GLY* 2.9 21.0 + - - +
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Residues in contact with GLU 44 (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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42B ALA* 4.5 13.3 - - - +
43B ALA* 1.3 76.8 - - - +
45B THR* 1.3 62.3 + - - +
53B PHE 3.7 0.9 - - - +
54B VAL* 3.5 3.2 - - - +
55B ALA* 2.8 42.1 + - + +
56B GLY* 4.9 4.0 - - - -
57B GLU* 5.8 2.0 - - - +
255B THR* 3.7 25.2 - - - +
276B SER 5.1 1.2 - - - +
278B LYS* 5.1 11.4 - - - -
46D LEU* 4.9 13.0 - - + +
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Residues in contact with THR 45 (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 ALA* 3.5 16.2 + - - +
24B ILE* 3.9 15.2 - - + +
25B SER* 2.9 21.0 + - - -
28B ILE* 4.8 0.3 - - - +
44B GLU* 1.3 75.4 + - - +
46B LEU* 1.3 61.6 + - - +
47B VAL* 3.9 14.4 - - + -
52B VAL* 3.8 28.5 - - + -
53B PHE 3.4 4.9 - - - +
54B VAL* 4.2 9.2 - - + +
254B LEU* 3.4 6.7 - - - +
255B THR* 2.7 38.5 + - - -
46D LEU* 5.3 2.0 - - - -
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Residues in contact with LEU 46 (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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44B GLU 4.3 0.2 - - - -
45B THR* 1.3 72.2 - - - +
47B VAL* 1.3 68.3 + - - +
48B THR* 3.9 26.2 - - + +
51B LEU* 4.5 1.3 - - + -
52B VAL* 3.6 1.0 - - - -
53B PHE* 2.8 47.0 + - + +
252B THR* 4.1 1.1 - - + -
253B GLY 3.4 2.5 - - - -
254B LEU* 3.9 24.2 - - + -
44D GLU* 5.1 4.5 - - + +
46D LEU* 4.2 26.9 - - + +
53D PHE* 3.7 39.9 - - + +
55D ALA* 3.9 15.0 - - + -
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Residues in contact with VAL 47 (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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17B PRO* 4.3 12.6 - - + +
20B LEU* 4.2 11.9 - - + -
21B ALA* 4.5 8.5 - - - -
24B ILE* 4.3 8.1 - - + -
45B THR* 3.9 18.4 - - + -
46B LEU* 1.3 80.4 - - - +
48B THR* 1.3 61.5 + - - +
51B LEU 3.7 3.6 - - - +
52B VAL* 4.0 19.3 - - + -
86B PHE* 4.6 2.0 - - + -
248B PRO* 3.4 33.7 - - + -
251B ASP 4.0 0.9 - - - +
252B THR* 3.3 5.7 - - - +
253B GLY 2.6 44.5 + - - +
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Residues in contact with THR 48 (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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92A ALA* 6.0 0.2 - - + -
46B LEU* 3.9 16.6 - - + -
47B VAL* 1.3 76.6 - - - +
49B THR* 1.3 76.4 + - - +
50B GLY 3.0 1.4 + - - -
51B LEU* 2.9 42.8 + - + +
86B PHE* 3.3 8.7 - - - -
248B PRO* 3.6 17.6 + - - -
252B THR* 3.1 25.7 + - - -
55D ALA* 4.6 8.1 - - + -
56D GLY 4.8 0.5 + - - -
57D GLU* 4.4 3.5 + - - -
96D ALA* 4.7 13.4 + - + +
98D ASP* 4.6 6.8 + - - -
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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