Contacts of the strand formed by residues 81 - 89 (chain V) in PDB entry 4N3E
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 81 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20V PHE* 3.5 10.1 - - - -
74V GLU* 3.0 39.0 + - + -
75V ILE* 3.8 0.9 - - - -
76V ASP* 3.1 59.2 + - + +
79V ASN 4.4 1.8 - - - +
80V PHE* 1.3 77.5 - - - +
82V CYS* 1.3 65.7 + - - +
83V LYS* 3.2 31.9 + - + +
102V GLU* 4.4 22.2 + - + +
103V VAL 3.1 12.3 - - - -
104V LYS* 4.0 23.8 - - + -
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Residues in contact with CYS 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V PHE* 4.0 13.9 - - + -
24V VAL* 4.1 14.6 - - + -
72V PHE* 3.9 19.3 - - - -
74V GLU 3.4 13.2 - - - -
75V ILE* 4.1 9.2 - - - -
81V TYR* 1.3 81.2 - - - +
83V LYS* 1.3 63.4 - - - +
84V TYR* 3.6 24.0 - - + -
101V TYR 3.8 0.6 - - - +
102V GLU* 3.4 2.9 - - - +
103V VAL* 2.5 51.7 + - + +
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Residues in contact with LYS 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115U LYS* 4.4 20.0 - - - +
73V ASP* 3.0 36.4 + - + +
74V GLU* 3.2 36.4 + - + +
81V TYR* 3.2 32.0 + - + +
82V CYS* 1.3 74.0 - - - +
84V TYR* 1.3 59.8 + - - +
100V VAL* 4.2 20.6 - - + -
101V TYR 3.2 10.8 - - - +
102V GLU* 3.7 26.2 - - + -
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Residues in contact with TYR 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V LEU 4.2 1.6 + - - -
24V VAL* 4.2 22.0 - - + -
27V ARG* 4.0 35.1 + - - -
70V HIS* 3.7 27.1 - + + -
71V LYS 3.2 14.8 - - - +
72V PHE* 3.7 23.8 - + + -
73V ASP* 4.0 1.1 - - - -
82V CYS* 3.6 19.1 - - + -
83V LYS* 1.3 73.9 - - - +
85V THR* 1.3 63.2 + - - +
100V VAL* 3.5 1.6 - - - +
101V TYR* 2.6 83.8 + + + +
103V VAL* 4.2 10.4 - - + +
203V SO4 5.1 1.6 + - - -
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Residues in contact with THR 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70V HIS* 3.3 10.4 - - - -
71V LYS* 2.8 44.4 + - + -
73V ASP* 2.9 23.6 + - - -
84V TYR* 1.3 72.3 - - - +
86V LEU* 1.3 72.4 + - - +
87V PHE* 3.5 12.2 + - + -
98V LYS* 3.8 30.1 + - + +
99V VAL 3.4 6.5 - - - +
100V VAL* 3.3 18.9 - - - +
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Residues in contact with LEU 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68V MET* 3.9 19.5 - - + -
69V LEU 3.8 10.5 - - - +
70V HIS* 3.8 32.9 - - + +
85V THR* 1.3 69.1 - - - +
87V PHE* 1.3 58.7 + - - +
88V GLU 4.4 2.5 - - - +
91V VAL* 4.5 17.9 - - + -
92V LEU* 3.4 32.7 - - + +
98V LYS* 3.1 10.7 - - - +
99V VAL* 2.7 48.8 + - + +
101V TYR* 4.1 18.3 - - + +
132V GLU* 5.9 1.3 - - - +
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Residues in contact with PHE 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V VAL* 3.5 38.6 - - + -
69V LEU* 3.2 48.9 + - + -
70V HIS 3.5 13.0 - - - -
71V LYS* 3.7 22.7 - - + -
85V THR* 3.8 13.0 - - + -
86V LEU* 1.3 74.8 - - - +
88V GLU* 1.3 68.5 + - + +
92V LEU* 3.8 4.7 - - - +
97V GLU 4.0 10.3 - - - +
98V LYS* 4.6 5.6 - - + -
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Residues in contact with GLU 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67V TYR* 2.7 40.4 + - - +
68V MET* 3.6 1.9 - - - -
69V LEU* 2.8 56.6 + - + +
86V LEU* 4.4 0.5 - - - +
87V PHE* 1.3 99.1 - - + +
89V GLY* 1.3 59.8 + - - +
92V LEU* 3.6 8.0 - - - +
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Residues in contact with GLY 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67V TYR* 3.5 26.5 - - - -
88V GLU* 1.3 79.5 - - - +
90V ASP* 1.3 60.7 + - - -
91V VAL* 3.2 6.0 + - - -
92V LEU* 3.0 26.3 - - - +
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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