Contacts of the strand formed by residues 75 - 80 (chain L) in PDB entry 3V4V
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 75 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L SER* 4.2 7.8 + - - -
23L CYS 3.9 1.3 - - - -
24L ARG* 3.8 31.6 + - - +
71L GLY* 3.1 18.2 - - - -
72L SER 3.2 9.6 + - - +
74L THR* 1.3 81.9 + - - +
76L PHE* 1.3 73.1 + - - +
77L THR* 4.1 10.4 - - - +
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Residues in contact with PHE 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L CYS* 2.7 52.0 + - + +
24L ARG 5.7 0.2 - - - -
25L SER* 4.4 1.6 - - - -
29L LEU* 3.5 23.1 - - + -
36L THR* 3.6 32.8 - - + -
38L LEU* 3.5 37.9 - - + -
40L TRP* 4.2 2.2 - - + -
56L ILE* 3.7 14.6 - - + -
70L SER 3.5 6.1 - - - +
71L GLY* 3.4 15.7 - - - -
72L SER 3.7 9.0 - - - -
73L GLY 3.3 30.3 - - - -
74L THR* 3.9 9.9 - - - -
75L ASP* 1.3 74.1 + - - +
77L THR* 1.3 66.3 + - - +
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Residues in contact with THR 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L SER* 5.7 3.6 - - - -
21L ILE 3.1 13.2 - - - +
22L SER* 4.5 7.4 - - - -
40L TRP* 3.6 8.0 + - - -
69L GLY* 3.6 1.7 - - - -
70L SER* 2.3 64.7 + - - +
71L GLY* 5.8 0.9 - - - +
75L ASP* 4.1 12.1 - - - +
76L PHE* 1.3 80.1 - - - +
78L LEU* 1.3 62.6 + - - +
79L LYS* 3.8 14.1 - - - -
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Residues in contact with LEU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L VAL 3.8 0.2 - - - +
20L SER* 3.2 4.3 - - - -
21L ILE* 2.7 45.3 + - + +
40L TRP* 3.7 43.2 - - + -
52L LEU* 4.4 5.8 - - + -
53L ILE* 4.0 27.1 - - + -
67L PHE* 5.0 8.1 - - + -
68L SER 3.9 14.4 - - - +
69L GLY* 4.1 2.7 - - - +
77L THR* 1.3 73.0 - - - +
79L LYS* 1.3 78.0 + - - +
80L ILE* 5.1 4.9 - - + -
91L TYR* 3.9 30.5 - - + -
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Residues in contact with LYS 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L GLN* 4.9 18.6 - - + +
19L VAL 3.3 5.4 - - - +
20L SER* 4.2 14.4 - - - -
66L ARG 3.3 2.2 - - - +
67L PHE* 3.4 3.8 - - - -
68L SER* 2.9 53.8 + - - +
70L SER* 3.9 14.0 + - - -
77L THR* 3.8 20.4 - - - +
78L LEU* 1.3 81.3 - - - +
80L ILE* 1.3 67.4 + - - +
81L SER* 5.3 0.7 - - - +
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Residues in contact with ILE 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ASP 3.5 1.7 - - - +
18L GLN* 3.4 3.8 - - - -
19L VAL* 2.7 42.9 + - + +
21L ILE* 6.3 2.5 - - + -
66L ARG* 3.5 13.9 - - + -
67L PHE* 3.8 21.1 - - + -
78L LEU* 5.1 6.3 - - + -
79L LYS* 1.3 78.0 - - - +
81L SER* 1.3 66.8 + - - +
83L ILE* 3.7 42.6 - - + +
87L ASP* 3.7 11.2 - - - +
91L TYR* 3.4 33.9 - - + +
109L LEU* 4.5 4.9 - - + -
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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