Contacts of the strand formed by residues 21 - 32 (chain A) in PDB entry 1H6H
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 ALA 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASP 3.6 3.0 + - - +
20A VAL* 1.3 85.9 - - - +
22A ILE* 1.3 61.6 + - - +
23A SER 4.7 0.2 - - - +
45A VAL* 3.9 24.2 - - + -
46A LYS 3.6 5.4 - - - -
47A THR* 4.3 3.8 - - + +
53A TYR* 5.6 0.4 - - - +
117A LEU* 3.9 37.2 - - + +
124A LEU* 5.3 2.1 - - - +
133A PHE* 4.2 18.6 - - + -
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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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13A PHE* 4.3 20.4 - - + -
20A VAL* 3.9 5.4 - - + +
21A ALA* 1.3 78.9 - - - +
23A SER* 1.3 64.3 + - - +
46A LYS* 2.8 29.1 + - + +
47A THR 3.8 15.3 - - - +
48A LYS* 3.7 26.7 - - + +
117A LEU* 4.0 12.4 - - - +
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Residues in contact with SER 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 ALA* 3.7 0.8 - - - +
22A ILE* 1.3 82.3 - - - +
24A ALA* 1.3 62.0 + - - +
25A ASN* 4.2 14.2 + - - -
44A GLU 4.4 1.2 + - - -
45A VAL* 3.5 6.1 - - - +
46A LYS* 3.1 54.9 + - - +
117A LEU* 3.8 8.3 - - - +
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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
----------------------------------------------------------
23A SER* 1.3 77.4 - - - +
25A ASN* 1.3 65.6 + - - +
43A ILE* 3.9 9.0 - - + -
44A GLU 3.3 7.6 - - - -
45A VAL* 4.5 2.7 - - + -
110A ASN* 4.3 6.1 - - - +
113A MET* 3.6 32.6 - - + +
114A LYS* 5.2 2.5 + - - +
117A LEU* 4.0 8.9 - - + +
133A PHE* 3.8 31.2 - - + -
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Residues in contact with ASN 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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23A SER* 4.2 13.5 + - - -
24A ALA* 1.3 86.0 + - - +
26A ILE* 1.3 66.6 + - - +
27A ALA* 3.5 0.7 + - - -
43A ILE* 4.1 2.8 - - - +
44A GLU* 2.9 40.9 + - + +
110A ASN* 3.7 15.2 + - - +
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Residues in contact with ILE 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 ASN* 1.3 73.4 - - - +
27A ALA* 1.3 62.1 + - - +
28A ASP* 3.5 25.1 - - - +
41A PHE* 3.9 26.5 - - + -
42A VAL 3.5 5.6 - - - +
43A ILE* 4.0 19.7 - - + +
62A PHE* 5.7 0.4 - - + -
106A ILE* 3.8 43.7 - - + +
109A LEU* 3.9 18.8 - - + -
110A ASN* 3.0 27.8 + - - +
113A MET* 4.1 7.2 - - + -
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Residues in contact with ALA 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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25A ASN 3.5 4.2 + - - +
26A ILE* 1.3 73.9 - - - +
28A ASP* 1.3 63.0 + - + +
42A VAL* 2.8 24.9 + - + +
44A GLU* 5.0 7.9 - - + +
54A LEU* 4.9 11.7 - - + -
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Residues in contact with ASP 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 ILE* 3.5 12.9 - - - +
27A ALA* 1.3 81.2 - - + +
29A ILE* 1.3 87.1 + - - +
30A GLU* 4.8 7.8 - - - +
42A VAL* 2.9 37.0 + - + +
106A ILE* 5.5 2.5 - - - -
151A GOL 4.7 8.9 + - - -
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Residues in contact with ILE 29 (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 ILE* 4.8 0.2 - - + -
28A ASP* 1.3 89.1 + - - +
30A GLU* 1.3 67.1 + - - +
39A PHE* 4.3 19.3 - - + -
40A VAL 3.3 7.9 - - - +
41A PHE* 3.7 31.6 - - + -
99A GLN* 4.7 1.3 - - + +
102A ALA* 4.3 9.0 - - + +
103A GLU* 3.9 31.6 - - + +
106A ILE* 3.8 22.4 - - + +
151A GOL 3.2 36.8 - - - +
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Residues in contact with GLU 30 (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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28A ASP* 4.8 7.6 - - - +
29A ILE* 1.3 80.4 - - - +
31A GLU* 1.3 63.6 + - - +
32A LYS* 3.8 25.3 + - - +
39A PHE* 3.5 7.0 - - - -
40A VAL* 2.9 38.3 + - + +
42A VAL* 3.8 22.8 - - + +
56A TYR* 4.1 19.8 - - - -
151A GOL 3.7 6.3 - - - +
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Residues in contact with GLU 31 (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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30A GLU* 1.3 74.4 - - - +
32A LYS* 1.3 74.7 + - - +
33A ARG* 3.7 27.4 + - + +
37A SER* 3.6 18.8 + - - -
38A HIS 3.8 4.0 - - - +
39A PHE* 3.5 35.7 - - + -
99A GLN* 5.1 4.0 + - - -
151A GOL 2.9 25.2 + - - +
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Residues in contact with LYS 32 (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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30A GLU* 4.3 24.1 + - - +
31A GLU* 1.3 73.9 - - - +
33A ARG* 1.3 64.2 + - - +
36A THR 4.1 1.2 - - - +
37A SER* 3.1 26.4 - - - -
38A HIS* 2.9 50.4 + - + +
40A VAL* 3.9 26.7 - - + -
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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