Contacts of the helix formed by residues 85 - 96 (chain K) 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 SER 85 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19K SER 3.7 29.0 + - - -
20K LEU 3.6 10.8 - - - -
21K PRO* 4.5 1.8 - - - -
22K LEU* 3.3 20.7 - - - +
78K TRP* 3.8 1.8 - - - -
83K GLY 3.6 2.9 + - - -
84K ALA* 1.3 75.1 - - - +
86K VAL* 1.3 63.3 + - - +
87K GLY* 3.6 1.9 + - - -
88K ARG* 3.1 25.6 + - - +
89K LEU* 3.4 16.5 + - - +
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Residues in contact with VAL 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K SER* 4.5 0.2 + - - -
20K LEU* 3.1 28.8 + - + +
21K PRO 3.3 26.5 - - - +
22K LEU* 4.3 7.6 - - - -
24K ALA* 4.7 4.3 - - + -
25K LEU* 4.4 18.4 - - + -
85K SER* 1.3 75.1 - - - +
87K GLY* 1.3 61.1 + - - +
89K LEU* 3.1 9.1 + - + +
90K LEU* 2.9 33.6 + - + +
109K ILE* 3.7 30.5 - - + +
113K CYS* 5.9 2.9 - - + -
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Residues in contact with GLY 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K SER* 4.2 10.1 + - - -
85K SER* 3.6 3.7 + - - -
86K VAL* 1.3 75.5 - - - +
88K ARG* 1.3 59.2 + - - +
90K LEU* 3.3 12.1 + - - +
91K GLU* 2.9 33.1 + - - +
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Residues in contact with ARG 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K GLU 4.6 7.1 + - - -
54K MET* 6.0 0.8 - - - +
55K ASP* 5.4 4.9 + - - -
78K TRP* 3.7 17.2 - - + -
83K GLY* 3.6 34.4 + - - +
85K SER* 3.1 24.4 + - - +
87K GLY* 1.3 74.3 - - - +
89K LEU* 1.3 58.6 + - - +
91K GLU* 3.3 25.0 + - - +
92K LEU* 2.9 56.1 + - + +
95K LYS* 5.2 6.7 - - - +
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Residues in contact with LEU 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LEU* 4.5 4.0 - - + -
25K LEU* 4.0 26.5 - - + -
33K LEU* 4.1 20.4 - - + -
50K LEU* 4.4 25.8 - - + -
54K MET* 4.9 2.5 - - - -
75K LEU* 4.2 19.7 - - + -
78K TRP* 3.9 21.2 - - + -
85K SER 3.4 11.4 + - - +
86K VAL* 3.1 12.2 + - + +
88K ARG* 1.3 79.4 - - - +
90K LEU* 1.3 59.4 + - + +
92K LEU* 3.3 2.5 + - + -
93K LEU* 2.9 40.5 + - + +
109K ILE* 5.6 6.1 - - + -
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Residues in contact with LEU 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K VAL* 2.9 26.9 + - + +
87K GLY* 3.3 8.9 + - - +
89K LEU* 1.3 79.7 - - + +
91K GLU* 1.3 59.1 + - - +
93K LEU* 3.8 10.3 + - + +
94K THR* 2.9 24.8 + - - -
102K LEU* 3.8 28.5 - - + +
105K LEU 5.3 2.2 - - - +
109K ILE* 3.8 40.2 - - + -
110K GLU* 6.4 2.2 - - + -
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Residues in contact with GLU 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K GLY 2.9 17.1 + - - +
88K ARG* 3.3 37.1 + - - +
90K LEU* 1.3 76.2 - - - +
92K LEU* 1.3 60.3 + - + +
93K LEU 3.3 0.2 - - - -
94K THR* 3.3 7.8 + - - -
95K LYS* 2.9 30.4 + - - +
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Residues in contact with LEU 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K LEU* 4.1 13.0 - - + -
53K GLU* 4.0 28.9 - - + +
54K MET* 3.7 31.9 - - + -
78K TRP* 4.2 8.1 - - + -
88K ARG* 2.9 50.7 + - + +
89K LEU* 3.9 4.3 - - - +
91K GLU* 1.3 75.9 - - + +
93K LEU* 1.3 60.6 + - - +
95K LYS* 3.8 30.5 - - + +
96K LEU* 3.1 32.1 + - - +
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Residues in contact with LEU 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU* 4.0 19.3 - - + -
37K LEU* 4.5 16.4 - - + -
50K LEU* 4.1 27.4 - - + -
89K LEU* 2.9 37.0 + - + +
90K LEU* 4.2 9.4 - - + +
91K GLU 3.3 0.2 - - - -
92K LEU* 1.3 76.4 - - - +
94K THR* 1.3 59.7 + - - +
96K LEU* 4.0 8.6 + - + +
97K GLY 3.7 0.7 + - - -
98K ARG* 3.2 36.7 + - + +
101K VAL* 3.8 25.1 - - + -
102K LEU* 3.7 17.9 - - + -
109K ILE* 6.1 1.3 - - + -
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Residues in contact with THR 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K LEU 2.9 16.0 + - - -
91K GLU* 3.3 11.9 + - - -
92K LEU 3.2 0.6 - - - -
93K LEU* 1.3 77.6 - - - +
95K LYS* 1.3 59.5 + - - +
96K LEU 3.2 0.2 - - - -
97K GLY* 2.9 20.1 + - - +
99K ASP* 4.5 14.3 + - - +
102K LEU* 3.4 18.2 - - + +
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Residues in contact with LYS 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K GLU* 3.4 27.9 + - - +
88K ARG* 5.2 6.5 - - - +
91K GLU* 2.9 19.5 + - - +
92K LEU* 3.8 24.6 - - + +
94K THR* 1.3 77.3 - - - +
96K LEU* 1.3 60.4 + - + +
97K GLY 3.1 0.9 + - - -
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Residues in contact with LEU 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LEU* 5.4 2.2 - - + -
45K ALA* 4.3 28.0 - - + +
46K ASP 4.7 2.5 - - - +
49K ALA* 3.9 19.1 - - + -
50K LEU* 3.7 42.4 - - + +
53K GLU* 3.7 29.2 - - + +
92K LEU 3.1 16.5 + - - +
93K LEU* 4.2 12.6 - - + +
94K THR 3.2 0.4 - - - -
95K LYS* 1.3 76.1 - - - +
97K GLY* 1.3 56.3 + - - +
98K ARG* 3.2 12.0 + - + +
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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