Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 3O5Z
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 TRP 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLU 4.8 3.4 + - - -
19A ARG* 3.5 62.3 - - + +
20A PRO* 3.7 28.7 - - + +
15B PHE* 3.6 28.5 - + - -
18B GLU* 4.5 8.5 - - - -
22B ASP* 4.3 2.2 - - - -
41B LEU* 3.8 12.6 - - - +
54B VAL 3.2 9.4 + - - +
55B GLY* 1.4 76.2 + - - -
57B MET* 1.3 62.7 + - - +
58B PRO* 4.7 0.3 - - - +
69B ASP* 4.4 8.5 - - + -
70B PHE* 3.5 12.1 - - - -
71B PRO* 3.4 44.7 - - + +
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Residues in contact with MET 57 (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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9B TYR* 4.2 15.5 - - + -
33B VAL* 4.1 16.2 - - + -
38B LEU* 3.9 23.3 - - + -
41B LEU* 4.5 0.4 - - + -
51B PRO* 3.7 21.5 - - + +
54B VAL* 3.5 28.0 - - + -
56B TRP* 1.3 71.8 - - - +
58B PRO* 1.4 67.4 - - + +
69B ASP* 3.2 5.0 - - - +
70B PHE* 2.8 60.5 + - + +
72B GLY* 3.6 30.3 - - - -
75B VAL* 4.6 0.7 - - + -
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Residues in contact with PRO 58 (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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33B VAL* 3.6 22.4 - - + +
34B SER 5.1 0.2 + - - -
37B ALA* 4.1 24.2 - - + +
41B LEU* 4.3 22.7 - - + -
56B TRP 4.7 0.7 - - - +
57B MET* 1.4 84.3 - - + +
59B GLY* 1.3 57.4 + - - +
68B GLY* 3.2 10.8 - - - +
69B ASP* 3.5 16.1 - - - +
70B PHE* 4.0 1.6 - - - -
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Residues in contact with GLY 59 (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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23B LEU* 3.9 5.6 - - - +
31B LEU* 5.5 0.4 - - - -
32B VAL 3.4 11.7 - - - -
33B VAL* 4.3 0.7 - - - -
58B PRO* 1.3 74.8 - - - +
60B LEU* 1.3 58.8 + - - -
67B ARG* 3.2 9.2 - - - +
68B GLY 2.8 31.8 + - - -
70B PHE* 3.7 18.8 - - - -
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Residues in contact with LEU 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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31B LEU* 3.5 4.3 - - - -
32B VAL* 2.9 55.2 + - + +
59B GLY* 1.3 75.0 - - - +
61B ASN* 1.3 59.7 + - - +
62B GLU* 3.8 16.1 + - + +
65B ARG* 3.5 26.5 - - + +
66B GLN 3.4 17.0 - - - +
67B ARG* 3.7 33.2 - - + +
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Residues in contact with ASN 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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23B LEU* 4.0 10.0 - - + +
24B GLU 3.3 24.9 + - - -
25B LEU* 4.2 0.2 - - - +
29B ASP* 3.6 23.7 + - - +
30B VAL 4.5 1.6 - - - +
31B LEU* 3.7 26.0 - - + +
59B GLY 4.3 0.2 - - - -
60B LEU* 1.3 70.7 - - - +
62B GLU* 1.3 56.1 + - - +
63B ARG* 3.4 20.0 + - - +
64B THR* 3.1 26.1 + - - +
65B ARG* 2.6 34.0 + - - -
66B GLN 3.0 12.3 + - - +
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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