Contacts of the helix formed by residues 83 - 105 (chain L) in PDB entry 6YOV
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 83 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81L LEU 3.9 1.0 + - - -
82L LEU* 1.3 76.1 - - - +
84L GLU* 1.3 65.7 + - - +
85L THR* 3.6 8.8 + - - -
86L GLU* 2.8 36.6 + - - +
87L LYS* 3.0 22.5 + - - +
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Residues in contact with GLU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L SER* 1.3 73.3 - - - +
85L THR* 1.3 61.6 + - - +
87L LYS* 3.2 10.8 + - - +
88L ARG* 2.7 71.2 + - - +
91L ILE* 5.0 6.2 - - + +
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Residues in contact with THR 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L SER* 3.2 8.7 + - - -
84L GLU* 1.3 88.0 + - - +
86L GLU* 1.3 59.1 + - + +
88L ARG* 3.6 5.8 - - + +
89L PRO* 3.1 24.1 - - - +
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Residues in contact with GLU 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L LEU 4.6 1.2 - - - +
82L LEU* 3.5 32.3 - - + +
83L SER* 2.8 42.7 + - - +
85L THR* 1.3 77.6 - - + +
87L LYS* 1.3 59.1 + - - +
89L PRO* 3.6 4.3 - - - +
90L PHE* 3.1 28.6 - - - -
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Residues in contact with LYS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L TRP* 3.1 66.9 + - + +
80L LYS* 4.0 18.8 + - - +
82L LEU* 3.3 26.8 + - + +
83L SER 3.0 20.3 + - - +
84L GLU* 3.6 7.4 - - - +
86L GLU* 1.3 75.6 - - - +
88L ARG* 1.3 66.1 + - - +
89L PRO* 3.4 0.2 - - - -
90L PHE* 2.9 17.3 + - - +
91L ILE* 2.9 24.8 + - + +
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Residues in contact with ARG 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84L GLU* 2.7 40.7 + - - +
85L THR* 3.6 9.0 - - + +
87L LYS* 1.3 72.2 - - - +
89L PRO* 1.3 65.9 - - + +
91L ILE* 3.0 20.7 + - - +
92L ASP* 2.8 63.6 + - - +
95L LYS* 4.0 13.9 - - - +
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Residues in contact with PRO 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L THR 3.1 17.3 - - - +
86L GLU* 3.6 10.8 - - - +
87L LYS 3.4 2.2 - - - -
88L ARG* 1.3 95.1 - - + +
90L PHE* 1.3 71.3 + - + +
92L ASP* 4.6 4.3 - - + +
93L GLU* 2.9 29.0 + - - +
96L ARG* 3.6 9.7 + - - +
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Residues in contact with PHE 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ALA* 3.5 22.8 - - - +
50L VAL* 3.9 15.2 - - + +
51L TRP* 3.5 52.5 - + + +
54L GLY* 6.2 2.2 - - - -
79L TRP* 4.0 2.9 - - + -
86L GLU 3.1 28.3 - - - -
87L LYS* 2.9 8.6 + - - +
89L PRO* 1.3 88.5 - - + +
91L ILE* 1.3 61.1 + - - +
93L GLU* 3.9 3.7 - - + +
94L ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L ALA* 3.6 24.2 - - + -
79L TRP* 4.2 6.7 - - + -
84L GLU* 5.0 7.0 - - + +
87L LYS* 2.9 38.7 + - + +
88L ARG* 3.4 26.0 - - - +
90L PHE* 1.3 78.8 - - - +
92L ASP* 1.3 59.9 + - - +
94L ALA* 3.4 4.5 + - - +
95L LYS* 3.2 36.0 + - + +
98L ARG* 5.8 0.2 + - - -
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Residues in contact with ASP 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L ARG* 2.8 52.0 + - - +
89L PRO* 4.4 0.4 - - - +
91L ILE* 1.3 74.9 - - - +
93L GLU* 1.3 60.3 + - - +
95L LYS* 3.0 36.6 + - + +
96L ARG* 2.8 57.5 + - - +
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Residues in contact with GLU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L VAL* 3.7 24.9 - - + -
53L ARG* 5.7 2.9 + - - +
89L PRO 2.9 22.2 + - - +
90L PHE* 3.9 3.8 - - + +
91L ILE 3.4 0.2 - - - -
92L ASP* 1.3 75.6 - - - +
94L ALA* 1.3 57.8 + - - +
96L ARG* 3.0 30.8 + - - +
97L LEU* 2.7 53.4 + - + +
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Residues in contact with ALA 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L MET 3.3 23.6 - - - +
46L ASN* 3.4 4.7 - - - +
47L ALA* 3.3 26.7 - - + +
50L VAL* 4.1 4.4 - - + +
90L PHE 2.9 13.1 + - - +
91L ILE 3.5 6.7 - - - +
93L GLU* 1.3 77.5 - - - +
95L LYS* 1.3 56.3 + - - +
97L LEU* 3.3 2.6 + - - +
98L ARG* 2.9 44.5 + - - +
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Residues in contact with LYS 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K GLY* 3.5 38.4 + - - +
88L ARG* 4.0 17.0 - - - +
91L ILE* 3.5 22.0 - - + +
92L ASP* 3.0 34.9 + - + +
94L ALA* 1.3 78.8 - - - +
96L ARG* 1.3 57.9 + - + +
98L ARG* 3.3 19.7 + - - +
99L ALA* 2.8 31.5 + - - +
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Residues in contact with ARG 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L PRO* 3.6 10.9 + - - +
92L ASP* 2.8 37.8 + - - +
93L GLU* 3.2 49.2 + - - +
95L LYS* 1.3 78.4 - - + +
97L LEU* 1.3 57.8 + - - +
99L ALA* 3.9 4.9 - - - +
100L LEU* 2.8 32.0 + - - +
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44L PRO* 3.9 11.8 - - + +
45L MET* 4.1 29.8 - - + +
50L VAL* 3.5 32.1 - - + -
93L GLU* 2.7 41.2 + - + +
94L ALA* 3.7 3.4 - - - +
96L ARG* 1.3 69.2 - - - +
98L ARG* 1.3 57.3 + - - +
100L LEU* 3.8 14.9 - - + +
101L HIS* 2.7 36.2 + - - +
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Residues in contact with ARG 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I G 3.4 10.9 + - - -
129I T 3.1 55.6 + - - -
130I T 5.4 3.4 - - - -
44L PRO* 3.7 29.0 + - + -
45L MET 4.4 5.6 + - - +
46L ASN* 3.5 25.5 - - - +
47L ALA* 4.4 3.0 - - - +
91L ILE 5.8 0.2 + - - -
94L ALA* 2.9 27.7 + - - +
95L LYS* 3.3 17.3 + - - +
97L LEU* 1.3 74.3 - - - +
99L ALA* 1.3 65.3 + - - +
101L HIS* 3.3 1.4 + - - +
102L MET* 3.0 41.4 + - + +
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Residues in contact with ALA 99 (chain L).
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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158K ILE* 4.3 23.3 - - - +
159K THR* 5.5 1.6 - - - +
95L LYS 2.8 21.0 + - - +
96L ARG* 3.9 5.4 - - - +
98L ARG* 1.3 72.1 - - - +
100L LEU* 1.3 57.9 + - - +
102L MET* 3.3 5.3 + - - +
103L LYS* 2.9 52.5 + - - +
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L ARG 2.8 19.9 + - - +
97L LEU* 3.8 16.2 - - + +
99L ALA* 1.3 77.1 - - - +
101L HIS* 1.3 61.4 + - - +
103L LYS* 3.2 17.5 + - + +
104L GLU* 3.0 53.8 + - + +
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Residues in contact with HIS 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L VAL* 3.5 22.6 - - + +
42L LYS 2.6 29.5 + - - -
43L ARG 4.8 0.2 - - - -
44L PRO* 4.1 23.1 - - + +
97L LEU 2.7 23.2 + - - +
98L ARG* 3.6 4.5 - - - +
100L LEU* 1.3 73.6 - - - +
102L MET* 1.3 60.7 + - + +
104L GLU* 3.2 10.3 + - - -
105L HIS* 2.8 37.8 + + - +
108L TYR* 3.4 33.4 - + - +
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Residues in contact with MET 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I T 4.0 25.4 - - - +
158K ILE* 6.4 2.5 - - - -
44L PRO* 5.2 7.6 - - + -
98L ARG* 3.0 32.0 + - + +
99L ALA* 3.9 4.9 - - - +
101L HIS* 1.3 79.7 - - - +
103L LYS* 1.3 60.6 + - - +
105L HIS 2.9 10.4 - - - +
106L PRO* 2.8 38.1 - - + +
108L TYR* 5.0 20.9 - - + +
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Residues in contact with LYS 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K THR* 5.7 7.9 - - - +
99L ALA* 2.9 41.5 + - - +
100L LEU* 3.2 17.6 + - + +
102L MET* 1.3 77.9 - - - +
104L GLU* 1.3 61.0 + - + +
106L PRO* 3.7 13.1 - - - +
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU* 3.0 45.6 + - + +
101L HIS* 3.6 11.6 - - - +
103L LYS* 1.3 76.9 - - + +
105L HIS* 1.3 80.7 + - + +
106L PRO* 3.5 5.8 - - - +
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Residues in contact with HIS 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L VAL* 3.8 41.0 - - + +
101L HIS* 2.8 27.6 + + - +
102L MET* 2.9 10.6 - - - +
104L GLU* 1.3 95.8 + - + +
106L PRO* 1.3 58.1 - - - +
107L ASP 3.2 2.9 - - - -
108L TYR* 2.9 41.3 + - + +
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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