Contacts of the helix formed by residues 51 - 65 (chain H) in PDB entry 1FQV
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 51 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8H SER* 3.7 2.0 - - - -
9H SER* 3.5 14.0 + - - +
10H ASP* 3.5 21.0 + - - +
49H ASN 4.4 0.2 - - - -
50H VAL* 1.3 79.9 - - - +
52H ALA* 1.3 58.7 + - - +
53H ALA* 2.8 32.9 + - - +
54H ILE* 3.4 29.1 + - - +
55H LEU* 3.0 25.8 + - - +
102H GLU* 6.1 0.2 - - - -
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H SER* 3.4 7.8 - - - -
10H ASP* 3.1 23.5 + - - +
12H GLU* 2.9 43.7 - - + +
14H PHE* 3.5 7.8 - - - -
51H ASN* 1.3 74.2 - - - +
53H ALA* 1.3 66.8 + - - +
55H LEU 4.1 0.2 - - - -
56H LYS* 3.3 23.0 + - - +
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ASN* 2.8 20.7 - - - +
52H ALA* 1.3 80.8 - - - +
54H ILE* 1.3 68.3 + - + +
56H LYS* 3.5 6.3 - - - +
57H LYS* 3.3 23.1 + - - +
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Residues in contact with ILE 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H VAL* 4.0 8.7 - - + -
51H ASN* 3.4 17.8 + - - +
53H ALA* 1.3 80.2 - - + +
55H LEU* 1.3 59.2 + - - +
57H LYS* 3.0 7.8 + - + +
58H VAL* 2.8 26.2 + - + +
99H THR* 3.9 29.2 - - + +
102H GLU* 3.6 34.1 - - + +
103H LEU* 3.5 17.3 - - + -
106H ALA* 3.4 32.8 - - + -
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 3.9 19.5 - - + -
8H SER* 4.2 16.4 - - - +
14H PHE* 4.0 28.3 - - + -
27H ILE* 5.3 0.7 - - + -
47H LEU* 3.5 30.1 - - + -
50H VAL* 3.5 13.2 - - + +
51H ASN 3.0 19.4 + - - +
54H ILE* 1.3 72.2 - - - +
56H LYS* 1.3 61.0 + - - +
58H VAL* 3.0 13.5 + - + -
59H ILE* 2.8 51.9 + - + +
110H LEU* 5.0 3.6 - - + -
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Residues in contact with LYS 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H GLU* 5.7 2.5 - - - +
14H PHE* 3.8 27.0 - - + -
52H ALA 3.3 18.3 + - - +
53H ALA* 3.5 7.2 - - - +
54H ILE 3.2 0.2 - - - -
55H LEU* 1.3 76.9 - - - +
57H LYS* 1.3 59.7 + - + +
59H ILE* 3.6 6.8 + - - +
60H GLN* 2.9 29.7 + - - +
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Residues in contact with LYS 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ALA 3.3 16.1 + - - +
54H ILE* 3.0 16.0 + - + +
56H LYS* 1.3 77.1 - - + +
58H VAL* 1.3 59.4 + - - +
60H GLN* 3.0 13.6 + - - +
61H TRP 2.8 27.2 + - - -
92H PHE* 3.1 65.7 + - + +
95H VAL* 4.0 17.4 - - - +
99H THR* 5.0 4.9 - - + -
103H LEU* 4.0 18.2 - - + -
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Residues in contact with VAL 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 6.3 0.7 - - + -
54H ILE* 2.8 36.5 + - + +
55H LEU* 3.5 14.6 - - + +
57H LYS* 1.3 72.3 - - - +
59H ILE* 1.3 58.8 + - + +
61H TRP* 3.4 5.3 + - - +
62H CYS* 2.9 39.8 + - - -
92H PHE* 5.2 0.2 - - - -
103H LEU* 4.2 8.5 - - + -
106H ALA* 4.2 13.7 - - + -
107H ALA 5.2 2.9 - - - +
110H LEU* 3.8 15.5 - - + -
112H ILE* 3.3 33.9 - - + -
115H LEU* 5.4 8.3 - - + -
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Residues in contact with ILE 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 3.9 6.3 - - + -
14H PHE* 3.6 29.4 - - + -
16H VAL* 3.1 42.8 - - + -
20H ILE* 4.5 3.5 - - + +
55H LEU* 2.8 40.8 + - + +
56H LYS* 3.7 5.2 - - - +
58H VAL* 1.3 74.8 - - + +
60H GLN* 1.3 58.8 + - - +
62H CYS* 3.8 5.3 - - - +
63H THR* 2.7 45.4 + - - +
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Residues in contact with GLN 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H LYS* 2.9 16.0 + - - +
57H LYS* 3.0 21.6 + - - +
59H ILE* 1.3 77.7 - - - +
61H TRP* 1.3 64.6 + - - +
63H THR* 3.2 7.1 + - - -
64H HIS* 3.0 22.0 + - - +
88H TRP* 3.8 21.6 + - + -
91H GLU* 5.1 2.3 - - - +
92H PHE* 3.4 23.9 - - - -
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Residues in contact with TRP 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H GLN* 4.5 6.1 - - - -
57H LYS 2.8 11.9 + - - +
58H VAL 3.7 3.8 - - - +
60H GLN* 1.3 73.6 - - - +
62H CYS* 1.3 69.7 + - - +
64H HIS* 3.5 1.4 - - - +
65H HIS* 2.8 77.3 + + + -
68H ASP* 6.0 0.2 - - + -
88H TRP* 3.7 18.8 - + - -
89H ASP* 3.5 12.3 + - - +
92H PHE* 3.3 42.8 - + + -
112H ILE* 4.4 7.9 - - + -
114H GLY* 3.4 12.3 - - - -
115H LEU* 3.3 55.3 - - + +
118H VAL* 3.8 17.3 - - + +
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Residues in contact with CYS 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ILE* 3.5 21.5 - - + +
23H GLN* 3.0 34.7 + - - +
24H SER 6.0 0.2 - - - -
58H VAL* 2.9 41.6 + - - +
59H ILE* 3.8 3.4 - - - +
61H TRP* 1.3 86.1 - - - +
63H THR* 1.3 61.5 + - - +
65H HIS 3.1 2.1 + - - +
66H LYS 2.7 25.3 + - - -
112H ILE* 4.1 16.4 - - - -
115H LEU* 5.6 0.2 - - - -
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Residues in contact with THR 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ILE* 3.7 30.3 - - + +
59H ILE* 2.7 30.1 + - - +
60H GLN* 3.4 7.6 - - - +
62H CYS* 1.3 76.2 - - - +
64H HIS* 1.3 57.3 + - - +
66H LYS* 2.7 38.6 + - + +
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Residues in contact with HIS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ARG* 2.7 60.2 + - + +
60H GLN 3.0 5.8 + - - +
61H TRP 3.5 9.0 - - - +
63H THR* 1.3 78.0 - - - +
65H HIS* 1.3 88.6 + + - +
66H LYS* 3.6 2.8 + - - +
68H ASP* 3.7 0.7 - - - +
86H PRO* 5.8 2.0 - - - +
88H TRP* 3.4 68.1 + + + +
89H ASP* 4.4 1.2 + - - -
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Residues in contact with HIS 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C ARG* 4.5 0.4 + - - -
23H GLN* 4.1 7.4 + - - +
61H TRP* 2.8 67.5 + + + +
62H CYS* 3.1 6.8 + - - +
63H THR 3.1 0.8 - - - -
64H HIS* 1.3 93.5 + + - +
66H LYS* 1.3 57.5 + - - +
67H ASP 3.0 3.6 - - - -
68H ASP* 2.7 64.7 + - + +
86H PRO* 5.0 6.7 - - - +
88H TRP* 4.1 0.2 - + - -
89H ASP* 2.9 35.7 + - - -
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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