Contacts of the strand formed by residues 37 - 47 (chain B) in PDB entry 2HVY
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 PHE 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.3 56.5 - - + +
30B VAL 3.6 8.5 - - - -
31B VAL* 4.0 9.0 - - + -
35B LEU 3.6 3.6 + - - -
36B GLN* 1.3 72.7 - - - +
38B VAL* 1.3 63.5 + - - +
39B GLY 3.3 28.3 - - - -
40B ILE* 5.2 2.0 - - + -
58B LYS* 3.6 46.7 - - + -
59B VAL* 3.4 20.2 - - + +
65B TYR* 4.7 1.7 + - - -
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Residues in contact with VAL 38 (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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16B LEU* 3.8 28.3 - - + -
30B VAL* 2.8 17.7 + - + +
32B ASP* 3.9 7.6 - - + +
36B GLN 3.5 15.0 - - - +
37B PHE* 1.3 75.9 - - - +
39B GLY* 1.3 57.9 + - - +
55B ILE* 5.2 0.9 - - + -
57B PRO* 3.8 2.1 - - - +
58B LYS* 2.9 22.5 + - - -
59B VAL* 3.6 13.9 + - + +
65B TYR* 3.7 38.4 - - + +
70B LEU* 3.8 28.7 - - + -
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Residues in contact with GLY 39 (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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29B ARG* 3.7 0.5 - - - -
30B VAL* 2.7 37.8 + - - +
37B PHE* 3.3 20.0 - - - -
38B VAL* 1.3 83.5 - - - +
40B ILE* 1.3 57.7 + - - -
55B ILE* 3.9 5.4 - - - -
56B LYS 3.2 12.8 - - - -
57B PRO* 4.2 0.4 - - - -
58B LYS* 3.9 5.2 - - - -
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Residues in contact with ILE 40 (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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27B ASN* 3.4 49.4 - - + +
28B ASP 3.5 4.9 - - - +
29B ARG* 5.4 2.2 - - + -
37B PHE* 5.2 2.7 - - + -
39B GLY* 1.3 74.8 - - - +
41B VAL* 1.3 66.2 + - - +
42B LYS* 3.4 12.5 + - - -
55B ILE* 3.4 6.2 - - - +
56B LYS* 2.7 58.9 + - + +
58B LYS* 3.7 32.3 - - + +
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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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4B LEU* 4.9 0.4 - - + -
24B PRO* 4.4 9.4 - - + -
25B SER 3.6 21.5 - - - +
26B LEU* 3.8 3.8 - - + +
27B ASN* 2.8 29.3 + - - -
28B ASP* 3.0 27.8 + - + +
30B VAL* 3.7 16.8 - - + -
40B ILE* 1.3 72.3 - - - +
42B LYS* 1.3 62.1 + - - +
43B ASP 4.1 3.8 - - - +
44B VAL* 4.0 18.6 - - + -
53B VAL* 3.7 22.4 - - + -
54B ALA 3.8 4.0 - - - -
55B ILE* 3.7 11.0 - - + -
72B VAL* 4.8 3.8 - - + -
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Residues in contact with LYS 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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143A PRO* 5.1 0.2 - - - +
15B PHE* 3.7 25.4 - - + -
26B LEU* 3.3 25.1 - - + +
27B ASN* 3.7 21.3 - - - +
40B ILE* 3.4 17.1 + - - +
41B VAL* 1.3 77.2 - - - +
43B ASP* 1.3 66.6 + - - +
54B ALA 2.9 7.7 + - - +
56B LYS* 3.7 33.2 - - + +
58B LYS* 5.0 4.2 - - - +
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Residues in contact with ASP 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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143A PRO* 3.6 14.9 - - - +
188A HIS* 5.3 2.3 + - - -
189A HIS* 2.8 33.3 + - - -
192A LEU* 4.8 4.5 - - + +
15B PHE* 6.1 0.7 - - + -
26B LEU* 4.1 4.5 - - - +
41B VAL* 3.8 1.2 - - - +
42B LYS* 1.3 81.8 - - - +
44B VAL* 1.3 81.3 + - - +
45B PHE* 4.0 8.0 - - + -
53B VAL* 3.4 4.9 - - - +
54B ALA* 2.8 46.4 + - + +
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Residues in contact with VAL 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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140A ILE* 3.5 38.6 - - + +
143A PRO* 3.9 24.1 - - + +
189A HIS* 5.5 0.5 - - - -
23B VAL* 3.9 12.6 - - + -
24B PRO* 3.5 37.0 - - + +
25B SER 5.3 0.7 - - - -
41B VAL* 4.0 17.0 - - + -
43B ASP* 1.3 86.1 + - - +
45B PHE* 1.3 65.1 + - - +
51B PRO* 4.0 9.2 - - + -
52B TYR 3.4 10.1 - - - +
53B VAL* 4.5 2.7 - - + -
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Residues in contact with PHE 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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135A PHE* 4.1 4.7 - + - -
140A ILE* 4.0 11.2 - - - +
189A HIS* 3.3 67.3 - + + +
192A LEU* 3.6 26.2 - - + -
193A ALA* 4.1 6.5 - - + -
17B ILE* 4.5 7.6 - - + -
43B ASP* 4.0 7.9 - - + -
44B VAL* 1.3 80.5 - - - +
46B GLY* 1.3 62.4 + - - +
51B PRO* 3.4 7.9 - - - +
52B TYR* 2.7 68.8 + + + -
54B ALA* 4.0 26.0 - - + -
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Residues in contact with GLY 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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135A PHE* 3.7 27.4 - - - -
139A ILE* 3.8 8.6 - - - +
140A ILE* 2.9 29.9 + - - +
45B PHE* 1.3 80.8 - - - +
47B PRO* 1.4 74.6 - - - +
52B TYR* 4.6 1.6 - - - -
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Residues in contact with PRO 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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134A GLU* 3.0 31.2 - - + +
135A PHE* 5.3 0.4 - - + -
136A GLU 5.4 2.5 - - - +
138A GLU 3.4 10.8 - - - +
139A ILE* 4.0 3.8 - - + -
19B ARG* 3.6 20.9 - - - +
46B GLY* 1.4 82.0 - - - +
48B VAL* 1.3 65.0 + - - +
49B LYS* 4.4 2.9 - - + +
50B MET* 3.2 24.9 - - + +
51B PRO* 3.0 27.4 - - + +
52B TYR* 4.5 9.2 - - + -
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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