Contacts of the strand formed by residues 59 - 64 (chain F) in PDB entry 1Z6Z
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 ARG 59 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLY* 4.5 23.2 + - - -
59D ARG* 5.2 8.3 - - - +
86D PRO* 5.7 5.2 - - - +
87D LYS* 5.5 16.8 - - + +
31F GLY* 3.4 29.0 + - - -
32F SER 3.1 13.6 + - - +
33F VAL* 3.4 20.7 - - + +
34F LEU 2.9 26.3 + - - +
58F LEU* 1.3 71.1 - - - +
60F VAL* 1.3 63.0 + - - +
61F VAL* 5.2 5.2 - - + -
84F PRO* 4.0 36.0 - - + +
85F ARG 4.5 9.1 + - - -
86F PRO* 4.6 4.0 - - - +
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Residues in contact with VAL 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D LYS* 5.1 10.0 - - - +
34F LEU* 3.4 11.9 - - + +
36F LEU* 3.8 27.4 - - + -
48F GLU* 3.8 41.6 - - + +
51F LEU* 3.9 24.2 - - + -
58F LEU* 3.7 21.5 + - + +
59F ARG* 1.3 74.9 - - - +
61F VAL* 1.3 70.9 + - - +
62F ARG* 4.1 2.6 + - + -
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Residues in contact with VAL 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ARG 6.1 1.1 - - - +
33F VAL* 4.3 19.7 - - + -
34F LEU 2.9 12.0 + - - +
35F VAL* 3.4 14.6 - - + +
36F LEU* 2.8 28.6 + - - +
59F ARG* 4.7 4.9 - - + +
60F VAL* 1.3 77.9 - - - +
62F ARG* 1.3 64.6 + - - +
63F VAL* 3.9 19.9 + - + -
79F ALA* 5.3 7.4 - - + +
83F LEU* 5.5 4.0 - - + -
84F PRO* 4.6 16.2 - - + -
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 3.7 8.7 - - + +
41F ASP* 2.9 30.5 + - - -
44F LEU* 3.5 44.9 - - + +
45F ARG* 3.6 13.1 - - - +
48F GLU* 2.7 32.4 + - + +
60F VAL* 4.1 5.5 + - + -
61F VAL* 1.3 77.0 - - - +
63F VAL* 1.3 63.2 + - - +
64F PRO* 3.6 9.9 - - + +
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Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F VAL* 4.0 21.5 - - + -
36F LEU 2.9 12.0 + - - +
37F SER* 2.8 32.7 + - - +
44F LEU* 4.1 2.8 - - - +
61F VAL* 4.0 9.2 - - + -
62F ARG* 1.3 78.1 - - - +
64F PRO* 1.3 63.3 - - + +
65F ALA* 3.4 7.0 + - + -
75F GLN* 4.0 11.7 - - + +
76F LEU* 3.8 39.9 - - + +
79F ALA* 3.8 21.8 - - + -
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Residues in contact with PRO 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ALA 3.2 10.3 - - - +
39F ARG 4.1 9.0 - - - +
41F ASP* 3.4 43.7 - - + +
44F LEU* 4.0 3.1 - - + -
62F ARG* 3.6 10.8 - - + +
63F VAL* 1.3 83.5 - - + +
65F ALA* 1.3 62.0 + - - +
75F GLN* 3.7 12.0 - - - +
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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