Contacts of the strand formed by residues 94 - 99 (chain D) in PDB entry 1VBF
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 LYS 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D GLN 3.5 0.2 + - - -
73D LYS* 3.2 45.1 - - + +
74D VAL 3.2 20.8 + - - -
92D VAL* 3.2 7.8 - - - +
93D ASP* 1.3 99.5 - - - +
95D VAL* 1.3 64.4 + - - +
96D VAL* 4.9 6.3 - - - -
117D ASN* 3.3 12.6 - - + +
119D LYS* 6.2 2.0 - - - -
132D GLU* 2.7 39.6 + - - -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL* 3.4 11.9 - - + +
76D GLU* 4.7 9.0 - - + -
85D THR* 4.3 21.3 - - + -
88D ILE* 3.7 32.5 - - + -
89D ALA* 4.0 21.3 - - - +
92D VAL* 4.3 5.8 - - + -
94D LYS* 1.3 84.1 - - - +
96D VAL* 1.3 76.9 + - - +
97D SER* 4.5 0.7 - - - +
117D ASN* 3.0 10.5 + - - +
118D ILE* 3.4 8.1 - - + +
119D LYS* 2.8 28.1 + - - +
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LYS* 4.7 6.1 - - + -
74D VAL 2.8 9.8 + - - +
75D LEU* 3.2 12.5 - - + +
76D GLU* 2.6 33.4 + - - +
94D LYS* 4.9 3.6 - - - -
95D VAL* 1.3 78.8 - - - +
97D SER* 1.3 54.8 + - - +
98D VAL* 4.9 0.7 - - + -
119D LYS* 3.6 8.1 - - + +
121D ILE* 3.4 30.5 - - + -
129D TYR* 3.8 25.4 - - + -
132D GLU* 4.2 21.3 - - + +
135D TYR* 3.8 22.0 - - + +
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Residues in contact with SER 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLU* 2.5 35.3 + - - -
79D THR* 2.3 31.8 + - - +
85D THR* 4.0 16.6 - - - -
95D VAL* 4.1 1.3 - - - -
96D VAL* 1.3 75.3 - - - +
98D VAL* 1.3 61.3 + - - +
118D ILE* 5.2 0.2 - - - -
119D LYS 3.1 7.2 + - - -
120D LEU* 3.6 13.8 - - - +
121D ILE* 2.9 25.7 + - - +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 4.3 18.8 - - + -
76D GLU 2.8 12.1 + - - +
77D ILE* 4.9 3.1 - - + -
78D GLY 2.8 29.1 + - - -
79D THR* 3.1 5.9 + - - -
96D VAL* 4.9 0.2 - - + -
97D SER* 1.3 76.4 - - - +
99D GLU* 1.3 60.7 + - - +
121D ILE* 3.5 19.5 - - + +
123D GLY* 3.1 36.1 - - - +
124D ASP 4.0 1.6 - - - +
125D GLY* 3.4 22.8 - - - +
128D GLY* 4.1 20.2 - - - +
129D TYR* 4.5 6.5 - - + -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ILE* 5.6 2.8 - - - +
78D GLY* 4.4 6.5 - - - -
79D THR* 3.4 31.1 + - + +
80D GLY* 3.5 18.8 + - - +
98D VAL* 1.3 72.9 - - - +
100D ILE* 1.3 64.8 + - - +
101D ASN* 2.5 42.8 + - - +
104D MSE 3.8 22.0 - - + +
105D TYR* 4.4 20.9 - - + +
108D ALA* 6.5 0.2 - - + -
121D ILE 2.9 10.2 + - - +
122D LEU* 3.2 8.5 - - - +
123D GLY 2.7 23.9 + - - -
125D GLY 5.6 0.2 - - - -
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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