Contacts of the strand formed by residues 68 - 76 (chain A) in PDB entry 2HUE
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU* 3.5 6.6 - - - -
30A CYS 2.9 36.4 + - - -
67A VAL* 1.3 79.2 - - - +
69A VAL* 1.3 63.6 + - - -
70A ASN* 3.1 10.3 + - - -
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Residues in contact with VAL 69 (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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7A LEU* 4.4 12.8 - - + -
27A THR* 3.7 27.6 - - + -
28A PHE 3.5 5.6 - - - +
29A GLU* 4.1 18.2 - - + +
67A VAL 5.1 1.0 - - - +
68A GLY* 1.3 74.1 - - - -
70A ASN* 1.3 66.9 + - - +
71A LYS* 5.0 6.3 - - + -
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Residues in contact with ASN 70 (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 3.8 0.5 - - - +
27A THR* 3.3 5.7 - - - +
28A PHE* 2.8 75.2 + - + -
30A CYS* 4.3 1.0 - - - +
66A PRO* 3.0 53.2 + - - +
67A VAL 4.6 0.4 - - - -
68A GLY 3.1 22.6 + - - -
69A VAL* 1.3 75.8 - - - +
71A LYS* 1.3 64.4 + - - +
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Residues in contact with LYS 71 (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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10A LYS* 5.0 5.1 - - - +
25A GLU* 3.6 31.5 + - + +
26A ILE 3.2 5.8 - - - +
27A THR* 3.4 31.6 - - + +
69A VAL* 5.0 6.3 - - + -
70A ASN* 1.3 77.5 - - - +
72A PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 72 (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 GLU* 3.4 5.3 - - - +
26A ILE* 2.8 81.1 + - + -
28A PHE* 4.2 13.2 - + - -
40A TRP* 3.5 41.1 - + + -
60A ILE* 3.6 36.8 - - + -
62A VAL* 5.9 2.7 - - + -
71A LYS* 1.3 78.5 - - - +
73A VAL* 1.3 76.2 + - - +
74A PHE* 3.9 15.9 - + - -
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Residues in contact with VAL 73 (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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12A LEU* 4.9 8.5 - - + -
24A PHE 3.1 14.1 - - - +
25A GLU* 4.3 13.7 - - + -
60A ILE* 5.5 2.6 - - - +
72A PHE* 1.3 90.8 - - - +
74A PHE* 1.3 67.8 + - - +
75A SER* 4.1 2.0 + - - +
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Residues in contact with PHE 74 (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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12A LEU* 5.6 0.2 - - - +
22A TYR 3.5 7.6 - - - +
23A GLU* 3.2 6.1 - - - +
24A PHE* 3.0 44.6 + + + +
26A ILE* 4.0 7.6 - - + +
40A TRP* 3.8 24.5 - - + -
42A LEU* 4.2 8.5 - - + -
58A ASP* 3.4 38.4 - - + -
59A SER* 4.0 1.6 - - - -
60A ILE* 4.0 25.6 - - + -
72A PHE* 3.9 21.0 - + - -
73A VAL* 1.3 82.6 - - - +
75A SER* 1.3 59.9 + - - +
76A ALA* 4.2 6.1 - - + +
97A LEU* 3.4 33.2 - - + -
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Residues in contact with SER 75 (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 PRO* 3.6 23.8 - - - +
22A TYR 3.3 5.8 - - - -
23A GLU* 4.2 12.0 + - - +
58A ASP* 3.7 7.1 + - - +
73A VAL* 4.0 3.2 + - - +
74A PHE* 1.3 75.4 - - - +
76A ALA* 1.3 58.3 + - - +
77A ASP* 4.0 4.0 + - - +
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Residues in contact with ALA 76 (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 PRO* 3.1 6.0 - - - +
22A TYR* 2.7 39.4 + - + +
42A LEU* 3.6 31.6 - - + -
57A LEU* 4.1 2.9 - - + -
58A ASP* 3.5 26.7 - - + +
74A PHE* 4.6 2.5 - - + -
75A SER* 1.3 72.5 - - - +
77A ASP* 1.3 70.1 + - - +
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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