Contacts of the strand formed by residues 105 - 110 (chain D) in PDB entry 3N3B
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 TRP 105 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D VAL* 3.2 22.9 - - + -
80D ALA* 3.4 25.6 - - + +
90D TYR 4.0 10.8 - - - -
91D GLY* 3.3 24.5 - - - -
94D GLY* 3.7 15.4 - - - -
95D ASP* 3.7 28.9 - - + -
98D ALA* 4.0 16.2 - - + +
103D VAL 3.7 1.6 + - - -
104D PRO* 1.3 71.4 - - - +
106D LEU* 1.3 63.3 + - - +
107D TYR 3.5 11.8 + - - -
108D ARG* 4.2 26.9 - - + -
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Residues in contact with LEU 106 (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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43D ILE* 4.2 28.9 - - + -
77D GLY* 4.2 19.3 - - - -
78D VAL 3.1 11.0 + - - +
79D ILE* 4.6 7.2 - - + -
104D PRO* 4.0 22.9 - - + +
105D TRP* 1.3 74.8 - - - +
107D TYR* 1.3 66.1 + - + +
124D GLY 6.1 0.7 - - - +
125D VAL* 6.2 1.1 - - + -
128D PHE* 4.1 32.3 - - + -
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Residues in contact with TYR 107 (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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78D VAL 4.0 2.2 + - - -
79D ILE* 3.4 19.9 - - + +
80D ALA 2.9 25.1 + - - -
105D TRP* 3.5 8.1 + - - -
106D LEU* 1.3 83.3 - - + +
108D ARG* 1.3 88.0 + - + +
109D PHE* 3.8 14.4 - + + -
116D SER 4.7 0.2 - - - -
117D ASP* 2.7 37.6 + - + -
120D ASN* 3.2 42.1 + - + -
121D VAL* 4.1 16.8 - - + -
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Residues in contact with ARG 108 (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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287A SER* 4.9 2.2 + - - -
80D ALA* 3.3 9.0 - - + +
84D ARG* 3.1 37.6 - - - +
90D TYR* 3.4 36.4 + - + +
91D GLY* 5.4 2.0 - - - -
105D TRP* 4.2 30.5 - - + -
107D TYR* 1.3 95.0 - - + +
109D PHE* 1.3 59.8 + - - +
117D ASP* 4.6 1.0 - - - +
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Residues in contact with PHE 109 (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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14D THR* 4.8 2.2 - - + -
17D PHE* 3.6 50.9 - + + -
45D ILE* 4.0 11.7 - - + -
79D ILE* 3.8 26.7 - - + -
80D ALA 3.0 16.0 + - - +
81D SER* 3.5 20.3 - - - -
82D GLY 3.1 22.2 + - - -
90D TYR* 3.4 14.2 + - - -
107D TYR* 3.8 8.3 - + + -
108D ARG* 1.3 75.6 - - - +
110D GLU* 1.3 60.5 + - - +
111D LEU 3.3 21.3 - - - -
113D GLY* 3.7 17.0 - - - -
117D ASP* 3.6 24.9 - - - +
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Residues in contact with GLU 110 (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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256A TYR* 2.7 32.1 + - - -
260A LYS* 2.9 38.2 + - + +
263A MET* 4.1 5.4 - - - +
82D GLY 3.3 6.7 - - - +
83D ASN* 3.6 0.6 - - - +
84D ARG* 3.1 26.1 + - - +
90D TYR* 3.5 23.5 + - + +
109D PHE* 1.3 75.9 - - - +
111D LEU* 1.3 65.3 + - + +
112D MET 3.2 0.2 + - - -
113D GLY* 2.8 30.7 + - - -
114D THR 4.8 0.2 + - - -
117D ASP* 4.5 4.8 + - - +
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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