Contacts of the helix formed by residues 91 - 102 (chain K) in PDB entry 1V8P
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 TYR 91 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34K LEU* 3.7 33.8 - - + +
38K GLU* 3.8 16.6 - - - +
89K THR* 3.2 8.6 + - - +
90K PHE* 1.3 77.9 - - - +
92K ASP* 1.3 63.7 + - - +
94K SER* 3.2 8.4 - - - -
95K TYR* 3.1 26.7 - - - -
34L LEU* 4.2 3.2 - - + +
37L TYR* 3.6 24.5 - - + -
38L GLU* 3.4 28.9 + - - +
41L ASN* 3.4 38.4 - - + +
91L TYR* 4.0 22.5 - + - -
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Residues in contact with ASP 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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48I ARG* 4.8 6.9 + - - -
38K GLU* 5.0 4.9 - - - +
88K LEU* 4.6 11.4 - - + +
89K THR* 3.3 21.9 + - - +
91K TYR* 1.3 76.8 - - - +
93K ALA* 1.3 55.2 + - - +
94K SER 2.6 16.0 + - - -
95K TYR* 2.8 25.2 + - - +
96K ALA* 3.2 8.1 + - - +
110K ASP* 4.1 18.2 - - - +
113K LEU* 3.9 33.4 - - + +
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Residues in contact with ALA 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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79K VAL* 3.2 29.8 - - - +
82K VAL* 3.7 12.6 - - + +
83K ALA* 3.5 25.1 - - + +
88K LEU* 4.1 8.4 - - + +
89K THR 2.8 19.6 + - - +
90K PHE 3.8 2.7 - - - +
92K ASP* 1.3 74.9 - - - +
94K SER* 1.3 59.0 + - - +
96K ALA* 3.8 7.3 - - - +
97K TYR* 3.4 17.8 + - - +
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Residues in contact with SER 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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32K LEU* 4.3 16.4 - - - -
34K LEU* 4.5 1.3 - - - -
74K PRO* 4.5 1.5 - - - +
79K VAL* 3.0 23.7 - - - +
90K PHE* 2.9 28.3 + - - -
91K TYR* 3.2 14.3 - - - -
92K ASP 2.6 2.2 + - - -
93K ALA* 1.3 76.7 - - - +
95K TYR* 1.3 57.0 + - - -
96K ALA 3.1 3.8 - - - -
97K TYR* 3.4 2.6 + - - +
98K VAL* 3.0 31.5 + - - +
37L TYR* 3.8 14.1 - - - -
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Residues in contact with TYR 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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6K LEU* 4.0 24.6 - - + +
7K VAL 4.4 2.2 - - - -
8K ASP* 3.4 36.8 - - + -
9K ALA 3.8 3.8 + - - -
32K LEU* 4.0 19.1 - - + -
34K LEU* 4.0 7.7 - - + +
35K THR* 3.1 28.6 + - - -
38K GLU* 2.4 30.3 + - - -
91K TYR 3.1 29.6 - - - -
92K ASP* 2.8 14.1 + - - +
94K SER* 1.3 77.6 - - - +
96K ALA* 1.3 57.8 + - - +
98K VAL* 4.1 1.6 - - - -
99K ALA* 3.1 30.1 + - - +
106K LEU* 3.8 23.2 - - + +
113K LEU* 4.6 3.8 - - + -
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Residues in contact with ALA 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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82K VAL* 4.0 17.3 - - + -
86K ARG* 4.1 15.5 - - - +
88K LEU* 4.6 7.9 - - + -
92K ASP 3.2 8.8 + - - +
93K ALA* 3.9 11.7 - - - +
94K SER 3.1 0.8 - - - -
95K TYR* 1.3 77.2 - - - +
97K TYR* 1.3 61.4 + - - +
99K ALA* 4.0 0.5 - - - +
100K GLU* 3.0 36.3 + - - +
106K LEU* 4.7 0.4 - - - +
117K THR* 4.2 20.8 - - - +
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Residues in contact with TYR 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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74K PRO* 4.2 5.8 - - + -
75K PRO* 3.5 28.8 - - + +
78K GLU* 2.8 53.8 + - + -
79K VAL* 3.9 23.1 - - + -
82K VAL* 4.0 19.9 - - + +
93K ALA 3.4 13.7 + - - +
94K SER 3.4 1.4 + - - -
96K ALA* 1.3 78.2 - - - +
98K VAL* 1.3 69.6 + - + +
100K GLU* 4.8 2.9 - - - -
101K SER* 3.0 45.1 + - - -
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Residues in contact with VAL 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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6K LEU* 3.2 27.8 - - + -
32K LEU* 4.1 13.0 - - + -
71K LEU* 3.8 22.0 - - + -
72K GLU* 4.6 5.2 - - + +
74K PRO* 3.1 36.8 - - + -
94K SER 3.0 14.1 + - - +
97K TYR* 1.3 80.5 - - + +
99K ALA* 1.3 68.1 + - - +
101K SER* 5.2 0.2 - - - -
102K SER* 2.9 35.4 + - - +
104K LEU* 4.5 2.5 - - + -
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Residues in contact with ALA 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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6K LEU* 4.3 9.4 - - + -
95K TYR 3.1 19.7 + - - +
96K ALA 4.0 1.6 - - - +
98K VAL* 1.3 83.8 - - - +
100K GLU* 1.3 56.9 + - - +
103K GLY* 3.0 8.1 + - - -
104K LEU* 2.6 50.8 + - + +
106K LEU* 4.3 16.4 - - + +
117K THR* 4.3 7.9 - - + -
118K LYS 5.9 0.2 - - - +
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Residues in contact with GLU 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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86K ARG* 2.7 48.2 + - - -
96K ALA 3.0 17.6 + - - +
97K TYR* 4.2 3.4 - - - +
99K ALA* 1.3 75.3 - - + +
101K SER* 1.3 63.7 + - - +
102K SER 3.2 1.7 + - - -
103K GLY* 3.5 9.2 + - - -
116K LYS 4.1 0.3 - - - +
117K THR* 4.8 3.3 - - + -
118K LYS* 2.8 40.1 + - + +
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Residues in contact with SER 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K TYR* 3.0 49.2 + - - -
98K VAL* 4.4 0.7 - - - -
100K GLU* 1.3 76.9 - - - +
102K SER* 1.3 61.1 + - - +
103K GLY 3.4 1.5 + - - -
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Residues in contact with SER 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K LEU* 5.6 2.4 - - - +
98K VAL* 2.9 25.1 + - - +
99K ALA 3.5 0.2 - - - -
101K SER* 1.3 82.6 + - - +
103K GLY* 1.3 67.9 + - - +
104K LEU* 3.2 25.7 + - - +
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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