Contacts of the helix formed by residues 93 - 101 (chain K) in PDB entry 6R1U
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 ASN 93 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79K THR* 3.2 6.7 + - - +
80K SER* 2.9 28.9 + - - +
81K ARG* 3.0 24.0 + - - +
83K TYR* 3.0 35.1 + - - -
92K CYS* 1.3 73.4 - - - +
94K GLU* 1.3 58.8 + - - +
96K PHE* 3.5 7.7 - - - +
97K ASP* 3.0 45.8 + - - +
101K ARG* 5.7 1.2 - - - +
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Residues in contact with GLU 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K SER* 3.8 10.2 + - - +
72K ARG* 3.3 44.7 - - + +
74K ALA* 3.9 6.2 - - - +
78K TYR 4.8 1.9 - - - +
79K THR* 2.8 33.2 + - - -
80K SER* 5.2 1.9 + - - -
92K CYS* 3.1 12.4 - - - -
93K ASN* 1.3 80.5 - - - +
95K CYS* 1.3 57.9 + - - +
97K ASP* 3.3 8.3 + - - +
98K HIS* 2.9 25.3 + - - +
104K LYS* 5.8 0.9 - - - -
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Residues in contact with CYS 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K CYS* 4.3 1.1 - - - -
67K ALA* 4.0 16.4 - - + -
68K SER 3.8 2.2 - - - -
69K ALA* 3.3 30.7 - - + +
70K SER* 3.4 10.1 - - - +
73K CYS* 3.6 7.6 - - - -
91K PHE* 4.8 4.5 - - + -
92K CYS* 3.2 6.0 + - - +
94K GLU* 1.3 75.5 - - - +
96K PHE* 1.3 68.3 + - - +
98K HIS* 3.1 21.5 + - - +
99K TYR* 3.5 16.1 - - + -
131K MET* 6.1 0.4 - - - -
903K ZN 2.3 36.3 - - - -
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Residues in contact with PHE 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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83K TYR* 3.6 47.1 - + + -
91K PHE* 3.7 30.2 - + + -
92K CYS 3.1 12.1 + - - +
93K ASN* 3.5 10.1 - - - +
95K CYS* 1.3 77.7 - - - +
97K ASP* 1.3 77.4 + - - +
99K TYR* 3.2 3.8 + - - +
100K TYR* 3.0 63.3 + + - +
101K ARG* 4.2 7.0 - - - -
127K PRO* 3.9 27.4 - - + +
128K LYS* 6.0 1.6 - - + -
131K MET* 6.5 0.2 - - - -
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Residues in contact with ASP 97 (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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23F ARG* 6.2 1.1 - - - -
93K ASN* 3.0 34.0 + - - +
94K GLU* 3.6 6.7 - - - +
96K PHE* 1.3 92.2 - - - +
98K HIS* 1.3 63.0 + - - +
100K TYR 4.3 0.7 - - - +
101K ARG* 2.9 60.2 + - + -
104K LYS* 3.2 23.2 - - - +
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Residues in contact with HIS 98 (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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69K ALA* 3.5 25.9 + - + +
70K SER* 3.7 21.4 + - - +
71K GLU* 4.5 8.1 + - - -
94K GLU 2.9 13.9 + - - +
95K CYS* 3.1 19.0 + - - +
97K ASP* 1.3 76.1 - - - +
99K TYR* 1.3 72.6 + + - +
104K LYS* 3.2 20.8 - - - +
105K ASP* 3.7 21.7 + - + -
106K GLY* 2.9 55.3 + - - -
107K TYR 3.4 0.5 + - - -
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Residues in contact with TYR 99 (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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67K ALA* 5.3 2.0 - - + +
69K ALA* 3.2 32.9 - - + +
95K CYS 3.5 18.2 - - - -
96K PHE* 3.2 6.4 + - - +
97K ASP 3.1 0.2 - - - -
98K HIS* 1.3 88.2 - + - +
100K TYR* 1.3 62.0 + - - +
101K ARG 3.4 0.7 - - - -
106K GLY* 2.9 31.6 - - - +
107K TYR* 3.3 25.4 - - - -
109K LYS* 4.2 12.8 - - + +
110K TYR* 3.7 24.0 - - + -
127K PRO* 6.1 3.4 - - + -
130K PHE* 3.8 27.1 - + + -
131K MET* 3.2 32.3 - - + -
135K GLN* 3.4 21.5 + - + +
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Residues in contact with TYR 100 (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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24F ASP* 5.1 14.2 + - - +
96K PHE* 3.0 48.9 + + + +
97K ASP* 4.3 1.1 - - - -
99K TYR* 1.3 79.1 - - - +
101K ARG* 1.3 91.3 + - - +
102K SER 3.9 0.5 + - - -
107K TYR* 3.7 12.1 - - - -
110K TYR* 4.4 17.8 - + - -
114K LYS* 6.0 3.4 - - - -
127K PRO* 3.6 32.1 - - + -
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Residues in contact with ARG 101 (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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23F ARG* 3.0 49.3 - - - +
24F ASP* 6.0 2.4 - - - +
93K ASN* 5.7 1.6 - - - +
96K PHE* 4.2 6.3 - - - -
97K ASP* 2.9 51.4 + - + +
100K TYR* 1.3 108.0 - - - +
102K SER* 1.3 65.3 + - - +
103K HIS* 3.2 14.8 - - + +
104K LYS* 3.1 26.6 + - + +
107K TYR* 3.2 14.3 - - - +
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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