Contacts of the helix formed by residues 99 - 105 (chain D) in PDB entry 6I3N
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 99 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D THR* 4.5 18.1 + - - +
97D GLY* 2.9 19.1 + - - +
98D ARG* 1.3 72.9 - - - +
100D ASP* 1.3 62.1 + - - +
101D VAL 3.3 1.3 - - - -
102D LEU* 4.0 17.8 - - + +
103D LEU* 3.7 24.8 + - + +
81H ARG 5.0 3.8 + - - +
82H PRO* 4.5 22.7 - - + +
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Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D PHE* 3.3 33.8 - - + -
98D ARG* 3.2 19.0 + - + +
99D ASP* 1.3 79.4 - - - +
101D VAL* 1.3 61.0 + - - +
103D LEU* 3.9 3.2 + - - +
104D GLU* 3.9 16.5 + - - +
21H PRO* 3.2 31.6 - - - +
79H GLN* 3.6 38.5 + - - +
80H GLY* 4.4 1.1 - - - -
81H ARG 5.3 3.4 + - - +
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Residues in contact with VAL 101 (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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33D LEU* 4.5 13.0 - - + -
36D PHE* 3.6 42.6 - - + -
37D LEU* 3.8 8.5 - - + -
93D LEU* 3.8 20.6 - - + -
98D ARG* 3.4 35.9 - - + +
100D ASP* 1.3 75.4 - - - +
102D LEU* 1.3 71.8 + - + +
103D LEU 3.2 2.5 - - - -
104D GLU 4.8 0.2 - - - +
105D LEU* 2.8 36.8 + - + +
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Residues in contact with LEU 102 (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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90D LEU* 3.8 26.7 - - + +
93D LEU* 3.7 31.4 - - + +
94D THR* 3.4 20.9 - - + +
98D ARG 3.5 20.4 - - - +
99D ASP* 3.8 15.3 + - + +
100D ASP 3.5 0.2 - - - -
101D VAL* 1.3 81.6 - - + +
103D LEU* 1.3 58.4 + - - +
104D GLU 3.5 0.2 - - - -
105D LEU* 4.8 1.8 - - - -
106D GLY* 3.3 24.1 + - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D ASP 3.7 16.3 + - - +
100D ASP* 4.4 3.8 - - - +
101D VAL 3.2 1.0 - - - -
102D LEU* 1.3 80.5 - - - +
104D GLU* 1.3 61.3 + - + +
106D GLY* 4.2 1.8 + - - -
107D PRO* 4.6 6.9 - - - +
19H SER 4.5 20.6 - - - +
20H LEU* 5.7 0.4 - - - -
21H PRO* 5.2 11.2 - - + -
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Residues in contact with GLU 104 (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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28D ARG* 5.4 5.5 + - - +
32D ARG* 3.7 29.7 + - + -
36D PHE* 3.2 29.4 - - + -
100D ASP 3.9 11.2 + - - +
101D VAL 3.4 2.0 + - - +
103D LEU* 1.3 82.1 - - + +
105D LEU* 1.3 59.3 + - + +
106D GLY 3.2 6.6 + - - -
107D PRO* 4.0 9.9 - - - +
108D SER* 4.4 6.6 + - - -
21H PRO* 4.6 6.6 - - + +
116H TYR* 2.7 29.8 + - - -
120H GLN* 4.0 20.8 + - + +
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Residues in contact with LEU 105 (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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28D ARG* 4.3 5.8 - - - +
29D VAL* 4.2 16.6 - - + +
32D ARG* 3.6 31.0 - - + +
33D LEU* 3.7 49.8 - - + +
36D PHE* 5.1 2.2 - - + -
90D LEU* 5.3 1.4 - - - +
101D VAL* 2.8 26.7 + - + +
102D LEU* 4.2 2.0 - - - -
104D GLU* 1.3 73.3 - - + +
106D GLY* 1.3 64.0 + - - +
107D PRO 3.7 0.4 - - - -
108D SER* 4.1 22.4 - - - -
109D ILE* 3.3 33.3 + - + +
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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