Contacts of the helix formed by residues 85 - 96 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19L SER 3.7 29.0 + - - -
20L LEU 3.6 11.0 - - - -
21L PRO* 4.5 1.8 - - - -
22L LEU* 3.3 19.6 - - - +
78L TRP* 3.8 1.0 - - - -
83L GLY 3.6 3.3 + - - -
84L ALA* 1.3 76.2 - - - +
86L VAL* 1.3 63.1 + - - +
87L GLY 3.6 1.9 + - - -
88L ARG* 3.1 25.7 + - - +
89L LEU* 3.4 16.3 + - - +
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Residues in contact with VAL 86 (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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19L SER* 4.5 0.4 + - - +
20L LEU* 3.1 27.5 + - + +
21L PRO 3.3 27.4 - - - +
22L LEU* 4.3 7.2 - - - -
24L ALA* 4.7 4.5 - - + -
25L LEU* 4.4 18.2 - - + -
85L SER* 1.3 74.8 - - - +
87L GLY* 1.3 61.1 + - - +
89L LEU* 3.1 9.9 + - + +
90L LEU* 2.9 32.7 + - + +
109L ILE* 3.7 31.2 - - + +
113L CYS* 5.9 3.4 - - + -
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Residues in contact with GLY 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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19L SER* 4.2 10.2 + - - -
85L SER* 3.5 3.7 + - - -
86L VAL* 1.3 76.3 - - - +
88L ARG* 1.3 60.0 + - - +
90L LEU* 3.3 12.2 + - - +
91L GLU* 2.9 33.7 + - - +
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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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53L GLU 4.6 7.1 + - - -
54L MET* 6.0 0.8 - - - +
55L ASP* 5.4 5.1 + - - -
78L TRP* 3.7 16.5 - - + -
83L GLY* 3.6 33.4 + - - +
85L SER* 3.1 24.0 + - - +
87L GLY* 1.3 74.8 - - - +
89L LEU* 1.3 58.5 + - - +
91L GLU* 3.3 25.7 + - - +
92L LEU* 2.9 56.8 + - + +
95L LYS* 5.2 6.8 - - - +
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Residues in contact with LEU 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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22L LEU* 4.5 3.4 - - + -
25L LEU* 4.0 26.7 - - + -
33L LEU* 4.1 19.3 - - + -
50L LEU* 4.4 24.5 - - + -
54L MET* 4.9 2.2 - - - -
75L LEU* 4.2 21.3 - - + -
78L TRP* 3.9 20.6 - - + -
85L SER 3.4 11.3 + - - +
86L VAL* 3.1 11.1 + - + +
88L ARG* 1.3 81.4 - - - +
90L LEU* 1.3 58.7 + - + +
92L LEU* 3.3 2.5 + - + -
93L LEU* 2.9 42.8 + - + +
109L ILE* 5.6 6.1 - - + -
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Residues in contact with LEU 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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86L VAL* 2.9 27.3 + - + +
87L GLY* 3.3 10.0 + - - +
89L LEU* 1.3 79.9 - - + +
91L GLU* 1.3 57.8 + - - +
93L LEU* 3.8 10.2 + - + +
94L THR* 2.9 24.1 + - - -
102L LEU* 3.8 28.8 - - + +
105L LEU 5.3 2.0 - - - +
109L ILE* 3.8 41.5 - - + -
110L GLU* 6.4 2.0 - - + -
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Residues in contact with GLU 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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87L GLY 2.9 17.9 + - - +
88L ARG* 3.3 37.4 + - - +
90L LEU* 1.3 76.9 - - - +
92L LEU* 1.3 60.6 + - + +
93L LEU 3.3 0.4 - - - -
94L THR* 3.3 7.6 + - - -
95L LYS* 2.9 30.1 + - - +
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Residues in contact with LEU 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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50L LEU* 4.1 12.3 - - + -
53L GLU* 4.0 29.6 - - + +
54L MET* 3.7 32.3 - - + -
78L TRP* 4.2 7.4 - - + -
88L ARG* 2.9 50.6 + - + +
89L LEU* 3.9 4.0 - - - +
91L GLU* 1.3 75.0 - - + +
93L LEU* 1.3 61.7 + - - +
94L THR 3.2 0.4 - - - -
95L LYS* 3.8 29.9 - - + +
96L LEU* 3.1 32.4 + - - +
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Residues in contact with LEU 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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33L LEU* 4.0 19.7 - - + -
37L LEU* 4.5 15.9 - - + -
50L LEU* 4.1 28.0 - - + -
89L LEU* 2.9 37.4 + - + +
90L LEU* 4.2 9.6 - - + +
91L GLU 3.3 0.2 - - - -
92L LEU* 1.3 77.4 - - - +
94L THR* 1.3 58.4 + - - +
96L LEU* 4.0 8.4 + - + +
97L GLY 3.7 0.9 + - - -
98L ARG* 3.2 36.6 + - + +
101L VAL* 3.8 24.7 - - + -
102L LEU* 3.7 17.9 - - + -
109L ILE* 6.1 1.3 - - + -
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Residues in contact with THR 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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90L LEU 2.9 16.4 + - - -
91L GLU* 3.3 11.9 + - - -
92L LEU 3.2 0.4 - - - -
93L LEU* 1.3 76.3 - - - +
95L LYS* 1.3 59.4 + - - +
96L LEU 3.2 0.4 - - - -
97L GLY* 2.9 20.1 + - - +
99L ASP* 4.5 14.5 - - - +
102L LEU* 3.4 17.7 - - + +
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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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53L GLU* 3.4 28.6 + - - +
88L ARG* 5.2 6.1 - - - +
91L GLU* 2.9 18.6 + - - +
92L LEU* 3.4 24.5 + - + +
94L THR* 1.3 78.0 - - - +
96L LEU* 1.3 60.0 + - + +
97L GLY 3.4 0.5 + - - -
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Residues in contact with LEU 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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37L LEU* 5.4 2.5 - - + -
45L ALA* 4.3 27.8 - - + +
46L ASP 4.7 2.2 - - - +
49L ALA* 3.9 19.3 - - + -
50L LEU* 3.7 42.0 - - + +
53L GLU* 3.7 28.7 - - + +
92L LEU 3.1 17.2 + - - +
93L LEU* 4.2 13.9 - - + +
94L THR 3.2 0.4 - - - -
95L LYS* 1.3 75.7 - - - +
97L GLY* 1.3 57.4 + - - +
98L ARG* 3.2 11.8 + - + +
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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