Contacts of the strand formed by residues 59 - 65 (chain B) in PDB entry 5H8N
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 THR 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B THR* 3.8 28.5 - - + +
47B GLY* 3.5 13.2 - - - +
48B PRO* 4.1 11.8 - - - +
57B ARG* 3.7 6.8 + - - +
58B HIS* 1.3 72.8 - - - +
60B VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 60 (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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46B THR* 3.5 5.6 - - - -
47B GLY 3.0 34.1 + - - +
49B ASN* 3.4 32.3 - - + +
58B HIS* 4.2 2.9 - - + +
59B THR* 1.3 78.9 - - - +
61B PRO* 1.4 81.7 - - + +
62B GLN* 3.5 17.1 + - + +
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Residues in contact with PRO 61 (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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22B PRO* 5.3 0.3 - - - +
23B THR* 3.7 22.9 + - + +
27B GLY* 5.7 3.6 - - - +
44B ILE* 4.3 17.7 - - + -
45B CYS 3.8 4.3 - - - +
46B THR* 4.1 13.0 - - + -
60B VAL* 1.4 92.3 - - + +
62B GLN* 1.3 62.7 + - - +
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Residues in contact with GLN 62 (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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20B VAL* 3.2 25.0 - - + +
21B LYS 3.6 13.1 - - - +
22B PRO* 4.9 5.3 - - + +
23B THR* 3.8 9.6 - - - +
44B ILE* 3.3 8.8 - - - +
45B CYS* 2.8 44.8 + - - +
47B GLY* 3.1 39.6 + - - +
48B PRO 3.5 11.2 + - - +
49B ASN* 5.6 2.6 - - - -
60B VAL* 3.8 12.7 + - + +
61B PRO* 1.3 78.6 - - - +
63B CYS* 1.4 58.8 + - - +
87B LEU* 3.8 5.2 - - - +
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Residues in contact with CYS 63 (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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19B TYR 3.6 1.2 - - - +
20B VAL* 3.5 5.7 - - - -
21B LYS* 2.8 46.6 + - + +
22B PRO 4.3 2.2 - - - -
23B THR* 3.8 25.6 - - - -
29B CYS* 2.0 56.1 - - + -
30B LYS 4.9 0.7 - - - -
42B LYS* 4.7 11.0 - - + +
43B VAL 3.4 3.6 - - - -
45B CYS* 3.9 1.5 - - - -
62B GLN* 1.4 71.5 - - - +
64B CYS* 1.3 60.1 + - - +
65B TYR* 4.5 2.6 - - + -
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Residues in contact with CYS 64 (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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11B THR* 4.5 4.9 - - - -
18B VAL* 4.2 17.0 - - + -
19B TYR 3.4 4.3 - - - +
20B VAL* 4.2 10.8 - - - -
42B LYS* 3.4 1.4 - - - -
43B VAL* 2.8 55.1 + - + +
45B CYS* 2.1 45.8 - - + -
63B CYS* 1.3 75.8 - - - +
65B TYR* 1.3 63.0 + - - +
69B ILE* 3.9 14.5 - - + +
85B VAL* 5.0 0.2 - - + -
87B LEU* 4.3 7.2 - - - -
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Residues in contact with TYR 65 (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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18B VAL* 3.5 3.1 - - - -
19B TYR* 2.7 63.9 + + + +
21B LYS* 3.6 44.0 - - + +
32B GLU* 3.8 25.2 + - - -
40B VAL* 3.8 15.3 - - + -
41B LYS 3.7 15.0 - - - +
42B LYS* 3.7 27.4 - - + -
63B CYS* 4.5 3.4 - - + -
64B CYS* 1.3 77.6 - - - +
66B GLY* 1.3 55.8 + - - +
69B ILE* 3.6 15.6 - - - +
285B TRP* 3.6 23.6 - + - -
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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