Contacts of the strand formed by residues 43 - 53 (chain B) in PDB entry 2H5X
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 GLU 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.2 40.8 + - - +
7B GLY* 3.3 19.7 - - - +
8B GLU* 4.3 2.5 - - + +
42B THR* 1.3 88.4 - - + +
44B ALA* 1.3 66.5 + - - +
45B ARG* 4.7 0.3 + - - +
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Residues in contact with ALA 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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6B ARG* 3.2 6.1 - - - -
7B GLY 2.9 30.8 + - - +
9B VAL* 3.7 22.9 - - + -
19B ILE* 3.6 11.7 - - + +
38B LEU* 4.5 21.8 - - + -
39B ARG 6.0 0.2 - - - +
42B THR* 3.6 2.4 + - + -
43B GLU* 1.3 79.6 + - - +
45B ARG* 1.3 61.8 + - - +
46B LEU* 6.1 0.4 - - + -
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Residues in contact with ARG 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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10A LEU* 4.0 33.8 - - - +
20A GLU* 4.4 7.3 + - - -
4B SER* 4.7 9.8 - - - -
5B VAL 3.2 12.3 - - - +
6B ARG* 3.3 30.8 - - + +
19B ILE* 6.1 0.2 - - - -
38B LEU* 5.7 0.5 - - - +
43B GLU* 4.7 0.4 + - - +
44B ALA* 1.3 75.0 - - - +
46B LEU* 1.3 75.2 + - - +
47B ILE* 4.0 24.1 - - - +
63B PRO* 5.6 2.4 - - - +
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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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4B SER* 3.1 5.2 - - - -
5B VAL* 3.0 32.9 + - + +
17B VAL* 4.1 16.4 - - + -
19B ILE* 5.2 9.4 - - + -
28B VAL* 3.3 35.0 - - + -
30B ALA* 4.8 1.1 - - + -
34B THR* 3.9 22.9 - - + -
37B THR* 5.8 0.2 - - - +
38B LEU* 4.4 21.3 - - + -
44B ALA* 6.1 0.7 - - + -
45B ARG* 1.3 82.0 - - - +
47B ILE* 1.3 65.2 + - - +
48B THR* 3.3 7.3 + - + +
61B GLY* 3.9 5.8 - - - -
62B PHE 3.7 22.7 - - - +
63B PRO* 4.9 3.4 - - + -
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Residues in contact with ILE 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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3B ALA 3.5 5.2 - - - +
4B SER* 4.1 9.2 - - - -
45B ARG* 4.0 31.2 - - - +
46B LEU* 1.3 73.9 - - - +
48B THR* 1.3 58.0 + - - +
61B GLY* 3.3 0.5 - - - -
62B PHE* 2.7 43.7 + - - +
63B PRO 4.0 4.9 - - - +
64B ASP* 3.6 29.8 - - - +
65B GLY* 3.7 11.9 - - - +
68B ARG* 2.9 46.0 - - + +
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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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2B ILE* 3.2 18.8 + - - +
3B ALA* 2.8 27.0 + - - +
4B SER 3.3 2.6 + - - -
5B VAL* 4.3 16.2 - - + -
28B VAL* 4.4 13.5 - - + -
46B LEU* 3.3 16.8 + - + +
47B ILE* 1.3 75.6 - - - +
49B ALA* 1.3 60.5 + - - +
59B LEU* 3.5 19.8 - - + +
60B TYR 3.1 8.1 - - - +
61B GLY* 4.0 13.2 - - - +
68B ARG* 3.0 24.3 + - - -
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Residues in contact with ALA 49 (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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2B ILE 4.5 0.4 - - - -
48B THR* 1.3 76.6 - - - +
50B MET* 1.3 59.9 + - - +
51B ILE* 3.1 14.2 - - + +
58B THR 3.6 0.2 - - - +
59B LEU* 4.6 0.4 - - - -
60B TYR* 2.9 27.5 + - - +
62B PHE* 4.4 0.2 - - + -
68B ARG* 4.0 14.4 - - + +
71B PHE* 3.9 20.2 - - + -
72B LEU* 3.8 29.8 - - + -
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Residues in contact with MET 50 (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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57A MET* 4.0 15.7 - - + -
1B MET* 3.5 49.6 + - + +
2B ILE* 3.7 48.4 + - - +
49B ALA* 1.3 70.2 - - - +
51B ILE* 1.3 62.2 + - - +
52B VAL* 3.8 30.4 + - + +
57B MET* 4.6 7.4 - - + +
58B THR 3.3 10.8 - - - +
59B LEU* 4.0 8.3 - - + -
1C MET* 4.0 15.5 - - - +
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Residues in contact with ILE 51 (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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49B ALA* 3.1 24.5 - - + +
50B MET* 1.3 73.6 - - - +
52B VAL* 1.3 62.5 + - - +
53B ARG* 3.6 40.1 + - + +
56B SER* 3.9 3.7 + - - +
57B MET* 3.6 1.6 - - - -
58B THR* 2.9 32.5 + - - -
60B TYR* 3.3 29.8 - - + +
71B PHE* 3.8 15.3 - - + -
72B LEU* 5.0 3.1 - - + -
75B LEU* 4.2 20.0 - - + -
82B PRO* 4.3 13.2 - - + -
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Residues in contact with VAL 52 (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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53A ARG 4.8 1.1 - - - +
54A GLU 4.2 3.6 - - - +
55A ASP* 3.2 15.0 + - - +
56A SER* 2.9 42.8 - - - +
57A MET* 4.3 12.6 - - + +
50B MET* 3.8 29.3 + - + +
51B ILE* 1.3 75.6 - - - +
53B ARG* 1.3 74.6 + - - +
56B SER 3.5 4.9 - - - +
57B MET* 3.8 29.8 - - + +
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Residues in contact with ARG 53 (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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54A GLU 3.6 9.9 - - - +
55A ASP* 3.7 34.5 + - - +
51B ILE* 3.6 29.6 + - + +
52B VAL* 1.3 95.9 + - - +
54B GLU* 1.3 66.8 + - - +
55B ASP 3.4 1.8 - - - +
56B SER* 2.8 35.4 + - - +
57B MET* 6.1 0.3 - - - +
75B LEU* 5.9 3.6 - - - +
82B PRO* 5.0 13.0 - - - +
52C VAL* 4.8 3.5 - - - +
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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