Contacts of the strand formed by residues 78 - 83 (chain F) in PDB entry 4NQD
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 TYR 78 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F LEU* 3.7 23.8 - - + -
40F LEU 3.3 15.0 - - - -
41F LYS* 3.6 45.3 + - + +
46F ILE* 4.5 6.3 - - + -
70F PHE* 3.6 35.4 - + + +
71F THR 4.2 8.0 + - - -
72F PRO* 4.9 5.6 - - + -
73F THR 5.3 0.2 - - - -
76F ASP* 3.7 27.9 + - + +
77F GLU* 1.3 75.1 - - - +
79F ALA* 1.3 55.7 + - - +
94F LYS* 3.3 6.8 - - - +
95F TRP* 2.6 72.7 + + + +
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Residues in contact with ALA 79 (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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9F VAL* 4.8 6.1 - - - -
23F LEU* 4.7 2.3 - - - +
39F LEU* 3.6 7.1 - - - +
40F LEU* 2.7 48.9 + - + +
78F TYR* 1.3 76.5 - - - +
80F CYS* 1.3 58.7 + - - +
92F ILE* 3.9 21.3 - - + -
93F VAL 3.3 12.6 - - - +
94F LYS* 3.8 9.4 - - + +
95F TRP 4.1 1.1 - - - +
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Residues in contact with CYS 80 (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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7F ILE* 4.0 4.6 - - + +
9F VAL* 3.5 17.3 - - + -
25F CYS* 2.0 52.9 - - + -
37F VAL* 3.7 19.5 - - - -
38F ASP 3.4 5.6 - - - -
39F LEU* 4.3 3.4 - - + -
40F LEU* 4.8 0.2 - - - -
79F ALA* 1.3 74.5 - - - +
81F ARG* 1.3 61.5 + - - +
82F VAL* 3.8 8.9 + - - -
91F LYS 3.4 4.7 - - - +
92F ILE* 3.4 2.4 - - - -
93F VAL* 2.9 29.8 + - - +
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Residues in contact with ARG 81 (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 GLU 3.6 1.2 - - - +
37F VAL* 3.4 3.1 - - - -
38F ASP* 2.6 74.9 + - + +
40F LEU* 3.4 41.0 - - + +
43F GLY 4.9 4.6 + - - -
45F ARG* 4.3 9.7 - - - +
79F ALA 4.3 0.4 - - - -
80F CYS* 1.3 72.1 - - - +
82F VAL* 1.3 62.6 + - - +
90F PRO* 3.9 24.2 - - + +
91F LYS 3.6 2.2 - - - +
92F ILE* 3.8 25.2 - - + +
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Residues in contact with VAL 82 (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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5F PRO* 4.1 11.9 - - + -
7F ILE* 3.6 22.7 - - + -
27F VAL* 3.7 31.9 - - + -
35F ILE* 3.8 28.9 - - + -
36F GLU 3.1 9.0 - - - +
37F VAL* 3.9 6.1 - - + -
80F CYS* 3.8 15.7 - - - -
81F ARG* 1.3 77.7 - - - +
83F ASN* 1.4 62.8 + - - +
87F LEU* 3.7 7.5 - - + +
90F PRO* 3.5 3.5 - - - +
91F LYS 3.0 31.7 + - - -
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Residues in contact with ASN 83 (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 ILE* 3.6 6.1 - - - +
36F GLU* 2.8 69.4 + - + +
82F VAL* 1.4 74.6 - - - +
84F HIS* 1.4 74.3 + - - +
87F LEU* 4.0 9.1 - - - +
88F SER 5.3 0.2 - - - -
89F GLN* 4.1 2.5 - - - +
90F PRO* 3.8 36.4 - - + +
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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