Contacts of the strand formed by residues 69 - 76 (chain H) in PDB entry 2ZJQ
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 VAL 69 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ILE* 4.6 2.7 - - + -
52H VAL* 4.2 16.4 - - + -
53H ALA 3.5 12.3 - - - +
54H SER* 4.4 1.3 - - - +
67H GLY 3.4 1.7 + - - +
68H ASP* 1.3 73.9 - - - +
70H VAL* 1.3 61.7 + - - +
106H ARG* 4.8 3.6 + - - -
1935X A 3.5 47.1 - - - +
2539X C 5.1 0.4 - - - +
2540X A 4.4 22.2 - - - +
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Residues in contact with VAL 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ILE* 5.4 2.2 - - + -
52H VAL* 4.4 2.9 - - - -
53H ALA* 2.5 48.4 + - + +
55H VAL* 3.9 18.2 - - + +
64H VAL* 5.5 1.8 - - + -
68H ASP* 3.8 13.5 - - + +
69H VAL* 1.3 76.9 - - - +
71H LYS* 1.3 83.7 + - - +
98H ILE* 3.2 33.0 - - + -
99H ILE 4.3 2.2 - - - +
106H ARG* 3.3 26.7 - - - +
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Residues in contact with LYS 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 4.2 17.0 - - + +
34H LEU* 4.4 22.5 - - + +
35H THR 6.0 0.4 + - - -
50H ILE* 4.5 12.8 - - + -
51H ILE 3.3 11.9 - - - +
52H VAL* 4.2 11.0 - - + -
70H VAL* 1.3 94.4 - - + +
72H ALA* 1.3 60.2 + - - +
98H ILE* 3.5 1.2 - - - +
99H ILE* 3.0 29.9 + - + +
100H ASN* 6.1 1.3 - - - -
101H ASN* 3.9 21.9 + - - +
106H ARG* 5.1 0.2 - - - +
2541X U 4.1 20.1 + - - -
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Residues in contact with ALA 72 (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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19H ILE* 3.9 27.8 - - + -
50H ILE* 3.1 8.7 - - - +
51H ILE* 2.8 37.9 + - + -
53H ALA* 5.1 2.0 - - + -
70H VAL* 4.0 0.4 + - + -
71H LYS* 1.3 75.0 - - - +
73H VAL* 1.3 62.2 + - - +
74H VAL 4.0 0.9 - - - -
96H ALA* 4.1 9.4 - - + -
97H VAL 3.7 7.2 - - - +
98H ILE* 3.9 13.9 - - + +
99H ILE* 4.2 3.6 - - - +
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Residues in contact with VAL 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLY* 4.4 7.4 - - - -
49H ASP 3.5 12.1 - - - +
50H ILE* 4.2 3.6 - - + -
72H ALA* 1.3 76.5 - - - +
74H VAL* 1.3 72.7 + - - +
75H VAL* 3.2 10.9 - - + +
96H ALA* 4.1 2.9 - - - -
97H VAL* 3.2 22.0 + - + +
99H ILE* 3.5 16.4 - - + -
118H LEU* 4.6 5.4 - - + -
123H PHE* 2.9 41.3 - - + -
126H ILE* 3.8 14.1 - - + -
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Residues in contact with VAL 74 (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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2H ILE* 4.1 23.6 - - + -
8H LEU* 4.2 10.1 - - + -
45H ALA* 4.0 21.5 - - + -
46H HIS 4.9 0.2 - - - +
47H VAL* 4.2 2.2 - - - -
48H GLY* 2.8 34.1 + - - +
49H ASP* 3.0 21.7 + - + +
51H ILE* 4.1 16.6 - - + -
72H ALA 4.0 0.6 - - - -
73H VAL* 1.3 75.6 - - - +
75H VAL* 1.3 60.3 + - - +
76H ARG 4.4 5.4 - - - +
77H THR* 4.1 17.7 - - + -
95H ALA 4.3 4.9 - - - +
96H ALA* 3.7 10.8 - - - +
118H LEU* 4.1 0.7 - - - +
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Residues in contact with VAL 75 (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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11H ALA* 4.3 9.6 - - + -
47H VAL* 3.2 6.5 - - - -
73H VAL 3.2 16.8 - - - +
74H VAL* 1.3 70.7 - - - +
76H ARG* 1.3 87.8 + - + +
95H ALA 3.1 19.4 + - - +
96H ALA* 4.0 1.1 - - - +
97H VAL* 3.7 20.4 - - + +
113H PRO 4.8 0.4 - - - +
114H VAL* 4.4 9.9 - - + -
115H ALA* 2.8 32.1 + - - +
118H LEU* 3.5 31.6 - - + -
126H ILE* 4.5 1.3 - - + -
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Residues in contact with ARG 76 (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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9H ASP* 5.4 0.8 - - - +
10H VAL 5.3 0.4 + - - -
11H ALA* 3.4 22.2 - - - +
47H VAL* 3.3 4.1 - - - +
74H VAL* 3.8 1.8 - - - +
75H VAL* 1.3 99.6 - - + +
77H THR* 1.3 62.3 + - - +
91H PHE* 3.8 32.1 - - + -
93H ARG 3.3 8.2 - - - +
94H ASN* 2.8 26.0 - - - +
95H ALA* 3.0 25.1 + - - +
111H PHE* 3.3 19.9 + - - +
112H GLY* 3.7 3.0 + - - -
113H PRO* 2.5 39.7 + - - +
114H VAL* 4.5 1.6 - - - +
75M GLU* 2.4 44.1 + - - -
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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