Contacts of the helix formed by residues 75 - 87 (chain L) 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 PRO 75 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62K LYS* 3.6 28.9 - - - +
74L PRO* 1.3 91.1 - - + +
76L LEU* 1.3 53.3 + - - +
77L ASP* 2.5 17.6 + - - +
78L GLU* 2.7 33.8 + - + +
79L VAL 3.5 5.5 + - - -
97L TYR* 3.4 24.0 - - + +
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Residues in contact with LEU 76 (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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36K ILE* 4.0 14.8 - - + +
40K GLY* 3.8 23.6 - - - +
43K LEU* 4.6 8.1 - - + -
58K SER* 3.9 35.2 - - - +
61K LEU* 3.8 15.3 - - + +
62K LYS* 4.7 11.7 - - + +
65K LEU* 3.4 31.2 - - + -
74L PRO 3.5 5.7 + - - -
75L PRO* 1.3 68.5 - - - +
77L ASP* 1.3 65.5 + - - +
79L VAL* 3.5 1.5 + - - -
80L LEU* 3.2 22.0 + - + +
90L PHE* 3.6 26.0 - - + -
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Residues in contact with ASP 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 5.7 0.7 - - - -
58K SER* 4.1 18.1 + - - -
59K ARG* 4.3 22.6 + - - +
62K LYS* 3.1 34.5 + - + +
75L PRO* 2.5 6.1 + - + +
76L LEU* 1.3 83.2 - - - +
78L GLU* 1.3 72.9 + - + +
80L LEU* 3.8 5.5 + - - +
81L ARG* 3.8 13.9 + - - +
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Residues in contact with GLU 78 (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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75L PRO* 2.7 29.3 + - + +
77L ASP* 1.3 82.4 - - + +
79L VAL* 1.3 65.3 + - - +
80L LEU 3.1 2.2 - - - -
81L ARG* 2.9 40.6 + - - +
82L VAL* 3.2 13.2 + - - +
97L TYR* 3.5 41.7 + - + +
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Residues in contact with VAL 79 (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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37K TYR* 6.0 0.7 - - + -
74L PRO* 3.8 30.1 - - + -
75L PRO 3.5 6.6 + - - +
76L LEU* 3.9 1.1 - - - +
78L GLU* 1.3 75.7 - - - +
80L LEU* 1.3 62.4 + - - +
82L VAL* 3.2 3.0 + - - +
83L ALA* 3.0 19.2 + - - +
90L PHE* 3.4 50.7 - - + +
93L ALA* 3.5 6.1 - - + +
94L SER* 3.5 31.9 - - - +
97L TYR* 4.2 15.9 - - + -
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Residues in contact with LEU 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K GLY 4.9 1.6 - - - +
43K LEU* 4.5 12.1 - - + -
44K TRP* 3.7 41.3 - - + +
47K ALA* 5.1 0.4 - - + -
54K TRP* 3.0 52.9 - - + +
58K SER* 4.2 8.5 - - - +
76L LEU* 3.2 19.5 + - + +
77L ASP 4.0 4.7 - - - +
78L GLU 3.1 0.4 - - - -
79L VAL* 1.3 79.6 - - - +
81L ARG* 1.3 57.0 + - - +
83L ALA* 4.2 0.9 - - + -
84L VAL* 2.8 45.5 + - + +
90L PHE* 3.9 14.1 - - + -
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Residues in contact with ARG 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 4.0 26.5 - - + -
77L ASP 3.8 7.2 + - - +
78L GLU* 2.9 45.2 + - - +
80L LEU* 1.3 77.9 - - - +
82L VAL* 1.3 77.6 + - - +
84L VAL* 3.7 0.5 + - - +
85L GLU* 2.7 70.4 + - - +
97L TYR* 5.5 4.8 - - - -
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Residues in contact with VAL 82 (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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78L GLU 3.2 11.0 + - - +
79L VAL 3.2 6.8 + - - +
81L ARG* 1.3 92.3 - - - +
83L ALA* 1.3 58.9 + - - +
85L GLU* 4.5 5.2 - - - +
86L ARG* 2.6 80.5 + - - +
88L LEU* 4.4 10.1 - - + -
93L ALA* 4.3 7.9 - - + +
96L ALA* 4.6 7.9 - - + -
97L TYR* 4.4 22.4 - - + +
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Residues in contact with ALA 83 (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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44K TRP* 3.7 17.8 + - + -
79L VAL 3.0 12.3 + - - +
80L LEU* 3.6 9.2 - - - +
82L VAL* 1.3 75.8 - - - +
84L VAL* 1.3 53.2 + - - +
87L GLY* 2.6 32.2 + - - -
88L LEU* 2.9 31.9 + - - +
89L THR 3.9 4.5 - - - +
90L PHE* 4.4 3.1 - - - -
93L ALA* 3.6 18.5 - - + +
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Residues in contact with VAL 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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112I GLU* 5.7 0.3 - - - +
44K TRP* 4.6 9.2 - - + +
47K ALA* 4.6 9.2 - - + -
54K TRP* 3.9 36.1 - - + +
80L LEU* 2.8 46.1 + - + +
81L ARG 3.9 4.0 - - - +
83L ALA* 1.3 78.9 - - - +
85L GLU* 1.3 65.4 + - + +
86L ARG 3.4 0.2 + - - -
87L GLY* 3.7 5.0 + - - -
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Residues in contact with GLU 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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54K TRP* 5.1 3.2 - - + -
81L ARG* 2.7 64.9 + - + +
82L VAL* 4.0 5.0 - - - +
84L VAL* 1.3 81.6 - - + +
86L ARG* 1.3 64.6 + - + +
87L GLY 4.0 0.2 + - - -
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Residues in contact with ARG 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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82L VAL* 2.6 52.7 + - + +
85L GLU* 1.3 82.2 + - + +
87L GLY* 1.3 58.9 + - - +
88L LEU* 4.1 15.5 - - + -
96L ALA* 4.3 8.2 + - - +
97L TYR* 6.1 0.8 - - - +
100L GLU* 2.7 40.6 + - - +
116L LYS* 2.6 72.5 + - + +
117L THR* 4.0 1.8 - - - +
118L LYS* 3.9 11.3 - - - +
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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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87I GLY 5.6 0.3 - - - +
112I GLU* 4.1 27.7 - - - +
44K TRP* 5.5 1.1 - - - -
48K ARG* 4.8 5.4 - - - -
1003K CL 3.9 17.0 - - - +
83L ALA 2.6 16.5 + - - -
84L VAL 3.7 4.4 + - - -
85L GLU 3.6 2.4 - - - -
86L ARG* 1.3 77.4 - - - +
88L LEU* 1.3 61.1 + - - +
112L GLU* 5.1 1.9 - - - +
116L LYS* 3.8 9.9 + - - -
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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