Contacts of the strand formed by residues 64 - 70 (chain H) in PDB entry 6NIL
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 LEU 64 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H PHE* 5.3 0.2 - - + -
20H LYS* 5.1 1.8 - - - +
21H LEU* 3.8 34.1 - - + -
58H VAL* 3.6 5.2 - - - +
59H ALA* 3.2 37.5 + - + +
62H THR* 3.2 17.0 - - - +
63H ASN* 1.3 76.4 - - - +
65H SER* 1.3 64.4 + - - +
66H LEU* 3.9 15.3 - - + -
9I ILE* 3.6 27.6 - - + -
10I VAL 4.5 1.6 - - - +
11I TRP* 3.5 39.7 - - + +
12I GLN* 3.2 7.3 - - - +
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Residues in contact with SER 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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56H ALA* 5.4 1.8 - - - -
57H PHE 3.3 15.0 - - - -
58H VAL* 4.5 3.1 - - - -
64H LEU* 1.3 77.5 - - - +
66H LEU* 1.3 64.8 + - - +
67H GLN* 2.8 26.9 + - - -
9I ILE* 3.2 16.6 - - - +
10I VAL 2.5 40.8 + - - +
12I GLN* 3.1 18.6 + - - +
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Residues in contact with LEU 66 (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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21H LEU* 5.8 1.8 - - + -
27H ILE* 6.1 1.6 - - + -
55H ILE 3.4 5.5 - - - +
56H ALA 3.5 0.2 - - - -
57H PHE* 3.0 41.9 + - + +
64H LEU* 3.9 20.0 - - + -
65H SER* 1.3 77.4 - - - +
67H GLN* 1.3 71.6 + - - +
68H PHE* 4.5 11.7 - - + -
101H MET* 3.7 30.1 - - + -
110H TRP* 4.2 38.1 - - + +
7I VAL* 5.3 9.2 - - + -
8I MET 4.9 1.1 - - - +
9I ILE* 3.8 20.2 - - + -
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Residues in contact with GLN 67 (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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54H GLU* 5.3 6.1 - - + -
55H ILE 3.5 5.4 - - - +
56H ALA* 3.3 23.0 - - + +
65H SER* 2.8 29.0 + - - -
66H LEU* 1.3 90.9 - - - +
68H PHE* 1.3 62.4 + - - +
69H PHE* 3.5 29.5 + - + -
6I GLN 3.8 0.3 - - - +
7I VAL* 3.6 23.3 - - - +
8I MET 3.8 15.6 + - - +
10I VAL* 3.3 26.3 - - + +
12I GLN* 5.8 1.0 - - - +
72I LEU* 3.8 28.2 - - + +
73I HIS* 6.5 0.7 - - + -
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Residues in contact with PHE 68 (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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54H GLU* 3.5 16.8 - - - +
55H ILE* 3.3 40.0 + - + +
57H PHE* 3.5 30.7 - + - -
66H LEU* 4.4 9.4 - - + -
67H GLN* 1.3 72.5 - - - +
69H PHE* 1.3 65.1 + - - +
84H GLU* 5.7 0.2 - - + -
85H TYR 5.2 1.1 - - - -
86H VAL* 4.6 3.1 - - + -
97H LEU* 4.2 13.9 - - + -
98H LYS 4.9 3.1 - - - -
99H ALA* 3.6 26.2 - - + -
110H TRP* 3.8 27.8 - + - -
5I TRP* 3.2 45.0 - + + -
6I GLN 4.2 2.5 - - - -
7I VAL* 3.6 12.6 - - + -
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Residues in contact with PHE 69 (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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54H GLU* 4.5 11.0 - - + -
67H GLN* 3.6 28.9 - - + -
68H PHE* 1.3 74.4 - - - +
70H PRO* 1.3 72.9 - - + +
73H TRP* 3.6 28.9 - + + -
5I TRP* 3.3 5.6 - - - -
6I GLN* 3.0 46.4 + - + +
8I MET* 4.4 17.5 - - + -
10I VAL* 4.5 4.3 - - + -
48I ASN* 4.0 13.5 - - - +
50I LYS* 4.2 9.9 - - + -
69I TYR* 3.6 36.8 - + - -
72I LEU* 4.0 22.2 - - + -
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Residues in contact with PRO 70 (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 GLY* 5.3 2.5 - - - -
52H ARG* 4.0 13.9 - - - +
53H SER 3.3 37.2 - - - +
69H PHE* 1.3 87.4 - - - +
71H ALA* 1.3 58.4 + - - +
72H SER* 3.1 16.8 - - - +
73H TRP* 2.9 52.9 + - + +
3I ASN* 5.4 7.6 - - + +
4I ARG 3.9 6.1 - - - +
5I TRP* 4.0 10.8 - - + -
6I GLN* 4.1 2.3 - - - +
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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