Contacts of the strand formed by residues 72 - 85 (chain H) in PDB entry 4AY9
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 72 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LYS* 2.3 30.7 + - - -
16H GLU* 5.0 0.5 + - - -
62H ARG* 3.6 7.9 - - - -
63H VAL* 2.7 46.5 + - - +
70H ALA 4.5 0.4 - - - -
71H ASP* 1.3 77.7 + - - +
73H LEU* 1.3 67.8 + - - +
74H TYR* 6.0 0.2 - - - +
84Y GLU* 5.7 4.3 - - - -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H THR* 4.0 20.4 - - + -
61H VAL 3.4 11.2 - - - +
62H ARG* 3.7 30.5 - - + +
63H VAL* 5.0 0.2 - - - -
72H SER* 1.3 82.0 + - - +
74H TYR* 1.3 62.2 + - - +
75H THR 4.3 0.2 - - - -
84Y GLU* 4.6 17.7 + - + +
85Y VAL* 3.2 46.7 - - + -
87Y GLU* 6.2 0.2 - - - +
110Y TYR* 5.3 2.9 - - + -
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Residues in contact with TYR 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G PRO* 5.9 2.1 - - - +
39G THR 4.1 7.1 + - - -
41G LEU* 3.3 37.3 + - + +
44G LYS* 3.7 23.2 + - + -
1052G NAG 4.7 10.3 - - - -
10H ILE* 5.5 1.3 - - + -
12H ILE* 3.8 29.8 - - + -
59H GLU 3.9 0.9 - - - +
60H THR* 3.5 2.0 - - - -
61H VAL* 3.0 33.5 + - + +
63H VAL* 4.0 20.4 - - + +
72H SER* 6.0 0.2 - - - +
73H LEU* 1.3 76.5 - - - +
75H THR* 1.3 70.6 + - - +
76H TYR* 3.6 31.4 + + + +
77H PRO* 5.8 0.7 - - - +
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Residues in contact with THR 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LYS* 5.2 1.2 + - - -
1052G NAG 4.2 28.6 - - - +
58H TYR* 3.3 35.5 - - + -
59H GLU 3.4 4.3 - - - +
60H THR* 2.5 30.3 + - - +
74H TYR* 1.3 84.4 + - - +
76H TYR* 1.3 62.6 + - - +
77H PRO* 4.7 0.5 - - - +
110Y TYR* 4.5 4.7 - - - +
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Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G PRO* 4.9 2.7 - - + -
10H ILE* 4.2 17.9 - - + -
12H ILE* 4.5 6.1 - - + -
23H ILE* 3.6 30.3 - - + +
24H ASN 4.7 0.9 + - - -
25H THR* 4.1 13.7 - - - -
58H TYR* 3.5 5.3 - - - -
59H GLU* 2.9 59.1 + - + +
61H VAL* 4.1 25.2 - - + +
74H TYR* 3.6 33.4 - + + +
75H THR* 1.3 75.3 - - - +
77H PRO* 1.3 79.0 - - + +
78H VAL* 3.2 22.6 - - + +
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Residues in contact with PRO 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G PRO* 3.7 12.1 - - + +
44G LYS* 5.8 2.0 - - - +
52G ASN* 3.7 31.4 - - + +
53G VAL* 4.1 8.7 - - + -
27H TRP* 3.3 29.2 + - + -
56H LEU* 4.2 11.9 - - + -
57H VAL 3.7 4.9 - - - +
58H TYR* 3.7 27.5 - - + +
74H TYR* 5.8 1.8 - - - +
75H THR 4.7 0.4 - - - +
76H TYR* 1.3 103.5 - - + +
78H VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H THR* 3.2 19.7 - - - +
26H THR* 4.0 8.5 - - - +
27H TRP* 4.1 5.8 - - - +
56H LEU* 3.0 5.3 - - - +
57H VAL* 2.7 51.6 + - + +
59H GLU* 3.8 26.5 - - + +
76H TYR* 3.2 36.6 - - + +
77H PRO* 1.3 72.8 - - - +
79H ALA* 1.3 71.8 + - - +
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 3.5 18.8 - - + +
26H THR* 3.1 23.1 + - - +
27H TRP* 3.7 35.2 - - + -
28H CYS* 4.5 5.2 - - - -
53H PHE* 4.3 4.9 - - + -
55H GLU 3.7 9.0 - - - +
56H LEU* 4.1 2.0 - - - -
78H VAL* 1.3 82.3 - - - +
80H THR* 1.3 63.8 + - - +
81H GLN 4.7 0.9 - - - +
82H CYS* 4.7 0.2 - - - -
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Residues in contact with THR 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 3.3 22.4 - - - +
55H GLU* 2.9 22.4 + - + +
56H LEU* 4.0 2.8 - - - -
57H VAL* 3.4 29.6 + - + +
78H VAL* 3.7 0.7 + - - +
79H ALA* 1.3 73.7 - - - +
81H GLN* 1.3 64.2 + - + +
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Residues in contact with GLN 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H LEU* 4.6 2.7 - - - -
53H PHE* 3.6 4.3 - - - +
54H LYS* 2.7 59.6 + - + +
55H GLU* 3.4 32.8 + - + +
79H ALA* 4.7 0.5 - - - +
80H THR* 1.3 84.0 + - + +
82H CYS* 1.3 65.0 + - - +
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Residues in contact with CYS 82 (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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3H CYS* 4.2 14.4 - - - +
4H GLU* 4.1 3.6 - - - -
5H LEU* 3.6 43.6 - - + +
27H TRP 3.8 1.6 - - - -
28H CYS* 2.1 55.0 - - + -
52H THR 3.6 3.4 - - - -
54H LYS* 4.4 2.4 + - - -
79H ALA* 4.7 0.7 - - - -
81H GLN* 1.3 82.1 - - - +
83H HIS* 1.3 63.7 + - - +
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Residues in contact with HIS 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H CYS* 3.3 13.1 - - - -
50H THR 3.4 1.0 - - - +
52H THR* 3.0 47.3 + - + -
53H PHE 3.9 8.5 - - - -
54H LYS* 3.2 56.6 - - - +
82H CYS* 1.3 77.5 - - - +
84H CYS* 1.3 67.6 + - - +
85H GLY* 3.6 13.7 + - - -
86H LYS 5.1 3.5 + - - -
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Residues in contact with CYS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H ASN* 3.8 16.2 - - - -
3H CYS* 3.7 15.4 - - - +
31H TYR 3.8 0.2 - - - -
32H CYS* 2.0 52.9 - - + -
33H TYR 4.9 0.4 - - - -
49H LYS* 3.8 24.6 + - + +
50H THR 3.3 4.9 - - - -
83H HIS* 1.3 79.0 - - - +
85H GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LYS* 3.4 16.4 - - - +
50H THR* 2.8 33.4 + - - +
52H THR* 5.0 1.3 - - - +
83H HIS* 3.6 19.4 + - - -
84H CYS* 1.3 76.0 - - - +
86H LYS* 1.3 65.7 + - - -
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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
------------------------------------------------------------
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