Contacts of the strand formed by residues 16 - 21 (chain I) in PDB entry 1H64
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 ASP 16 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15I LYS* 1.3 77.8 - - - +
17I VAL* 1.3 74.7 + - - +
28I ARG* 2.8 48.3 + - - -
29I GLY* 3.1 27.3 + - - +
30I ARG* 4.2 3.2 - - + +
72I PRO* 3.9 0.9 - - - +
73I THR* 2.7 39.8 + - - +
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I SER* 3.8 28.3 - - - -
15I LYS 3.9 4.5 - - - +
16I ASP* 1.3 87.1 + - - +
18I LEU* 1.3 60.2 + - - +
19I VAL* 4.4 9.6 - - + -
27I PHE 3.9 0.7 - - - +
28I ARG* 3.6 5.1 - - - -
29I GLY 2.8 27.8 + - - +
31I LEU* 4.0 14.8 - - + -
42I LEU* 3.6 30.8 - - + +
70I ILE* 4.3 15.9 - - + -
71I SER 3.4 7.6 - - - +
72I PRO* 4.0 11.4 - - + -
73I THR* 4.3 1.1 - - - -
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Residues in contact with LEU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 1.3 72.1 - - - +
19I VAL* 1.3 61.7 + - - +
20I ILE* 4.1 16.9 - - + +
26I GLU* 3.3 35.4 - - + +
27I PHE 3.6 13.5 - - - +
28I ARG* 4.5 12.8 - - - +
48I ILE* 4.6 3.1 - - + -
69I ALA 4.0 0.5 - - - +
70I ILE* 3.1 7.3 - - - +
71I SER* 2.8 42.5 + - - +
73I THR* 4.2 11.1 - - + +
55J LYS* 6.1 3.4 - - + -
57J TYR* 4.1 28.5 - - + -
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Residues in contact with VAL 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 4.4 10.8 - - + -
18I LEU* 1.3 76.5 - - - +
20I ILE* 1.3 60.1 + - - +
21I LEU* 3.5 21.8 + - + +
26I GLU* 3.2 5.6 - - - -
27I PHE* 2.8 40.5 + - + +
40I VAL* 4.4 13.5 - - + -
42I LEU* 4.2 22.0 - - + -
62I ILE* 4.4 12.6 - - + -
67I VAL* 3.9 23.1 - - + -
69I ALA 3.6 3.4 - - - -
70I ILE* 4.1 13.2 - - + -
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I LEU* 4.1 19.7 - - + +
19I VAL* 1.3 70.9 - - - +
21I LEU* 1.3 67.4 + - - +
25I PHE 4.5 4.3 - - - +
26I GLU* 4.1 13.9 - - - +
67I VAL* 3.8 1.6 - - - +
68I LEU* 2.8 45.6 + - + -
69I ALA* 2.9 23.7 + - + +
71I SER* 5.7 1.6 - - - -
25J PHE* 6.1 0.4 - - + -
27J PHE* 4.6 2.9 - - + -
47J MET* 4.5 14.6 - - + -
57J TYR* 3.8 34.8 - - + +
60J ILE* 4.1 17.5 - - + -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H LEU* 3.3 36.1 - - + -
19I VAL* 3.5 30.4 + - + +
20I ILE* 1.3 79.5 - - - +
22I LYS* 1.3 57.8 + - - +
23I LYS* 3.0 15.7 + - + +
24I GLY* 3.6 9.2 + - - -
25I PHE* 3.3 34.2 + - + +
26I GLU 4.4 0.4 - - - +
27I PHE* 3.4 27.4 - - + -
62I ILE* 4.4 5.4 - - + -
66I ASN* 3.8 16.8 - - + +
67I VAL* 4.2 8.3 - - + -
68I LEU* 3.5 14.0 - - - +
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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