Contacts of the strand formed by residues 20 - 28 (chain H) in PDB entry 6AHU
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 HIS 20 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ASN* 5.3 3.8 + - - -
17H SER* 4.4 7.0 + - - -
18H GLU* 5.6 0.2 - - - -
19H TYR* 1.3 87.6 + - - +
21H TYR* 1.3 65.2 - - - +
22H MET* 4.5 5.4 - - - +
75H LEU 3.8 0.5 - - - +
76H ARG* 3.3 19.7 - - - +
77H ILE 3.1 13.1 + - - +
78H CYS 3.9 2.9 - - - -
79H SER* 3.6 34.9 - - - -
82H LEU* 3.7 36.7 - - + +
107H VAL* 5.4 2.2 - - + +
109H PRO* 3.4 18.2 - - + +
11L PRO* 3.5 37.0 - - + +
13L HIS* 3.8 16.1 + + - -
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Residues in contact with TYR 21 (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 TYR* 4.7 8.1 - - + -
20H HIS* 1.3 74.4 - - - +
22H MET* 1.3 67.1 + - - +
64H LEU* 4.3 8.3 - - + -
74H ILE* 3.9 10.5 - - + -
75H LEU 3.4 2.0 - - - -
76H ARG* 3.2 47.5 + - + -
107H VAL* 3.7 3.6 - - - +
108H SER 2.9 35.0 + - - +
109H PRO 3.2 28.7 - - - -
110H PHE* 3.7 6.7 - - - -
111H LEU* 3.6 39.9 - - + +
114H LEU* 3.7 13.2 - - + -
242L ASP* 2.6 34.4 + - - -
264L TYR* 4.0 9.5 - + - -
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Residues in contact with MET 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H HIS 4.5 3.4 - - - +
21H TYR* 1.3 81.2 - - - +
23H LYS* 1.3 63.0 + - - +
24H VAL* 3.8 4.4 + - + +
74H ILE* 3.3 9.9 - - - +
75H LEU* 2.9 35.0 + - + +
76H ARG* 6.3 0.2 - - - -
82H LEU* 4.4 10.8 - - + -
85H LEU* 3.7 30.5 - - + -
86H TRP* 3.3 37.2 - - + +
102H PHE* 4.7 15.3 - - + -
104H VAL* 4.4 21.1 - - + -
106H GLN 4.0 4.3 - - - -
107H VAL* 3.8 19.5 - - + -
114H LEU* 3.9 4.5 - - - -
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Residues in contact with LYS 23 (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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22H MET* 1.3 74.9 - - - +
24H VAL* 1.3 66.6 + - - +
25H CYS* 4.0 0.4 + - - -
72H SER* 5.6 8.7 - - - -
73H ALA 3.9 4.7 - - - +
74H ILE* 4.9 1.8 - - + -
102H PHE* 5.4 0.2 - - - -
104H VAL* 4.0 12.3 - - - +
105H ILE* 3.8 49.0 + - + +
106H GLN* 3.1 49.2 + - + +
114H LEU* 3.8 14.8 - - + +
117H ASN* 5.4 4.8 + - - +
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Residues in contact with VAL 24 (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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22H MET* 4.1 9.0 - - + +
23H LYS* 1.3 80.3 - - - +
25H CYS* 1.3 64.1 + - - +
26H LEU* 4.5 7.4 - - + -
40H PHE* 3.7 23.1 - - + -
71H LEU 4.8 1.6 - - - +
72H SER* 3.3 26.9 - - - -
73H ALA* 2.9 29.9 + - + +
75H LEU* 3.8 35.0 - - + -
102H PHE* 3.6 29.2 - - + -
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Residues in contact with CYS 25 (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 LYS* 4.0 0.8 + - - -
24H VAL* 1.3 75.3 - - - +
26H LEU* 1.3 80.6 + - - +
27H GLU* 4.9 10.5 - - - -
70H THR 5.6 4.3 - - - -
71H LEU 4.0 3.6 - - - -
72H SER* 5.7 0.7 - - - -
102H PHE* 3.9 4.4 - - - -
103H ARG* 3.1 42.3 + - - +
105H ILE* 3.8 28.0 - - + -
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Residues in contact with LEU 26 (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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24H VAL* 4.5 2.9 - - + -
25H CYS* 1.3 82.4 - - - +
27H GLU* 1.3 68.9 + - - +
28H PHE* 4.2 9.6 - - + -
35H LEU* 3.9 24.7 - - + -
40H PHE* 3.7 32.1 - - + -
43H LEU* 5.9 5.4 - - + -
66H TYR* 5.4 1.8 - - + +
70H THR 5.1 2.8 + - - +
71H LEU* 3.7 44.9 + - + +
100H CYS* 5.1 6.3 - - - -
101H ALA 4.3 8.7 - - - +
102H PHE* 3.7 29.4 - - + -
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Residues in contact with GLU 27 (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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25H CYS* 4.9 10.5 - - - -
26H LEU* 1.3 81.5 - - - +
28H PHE* 1.3 63.1 + - - +
100H CYS* 3.3 21.7 - - - -
101H ALA* 3.4 22.8 + - + +
103H ARG* 2.7 53.4 + - + +
27J HIS* 4.5 14.0 + - - -
28J LEU* 5.4 0.2 - - - +
195J LEU* 3.8 14.4 - - + +
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Residues in contact with PHE 28 (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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26H LEU* 4.2 13.9 - - + -
27H GLU* 1.3 76.9 - - - +
29H GLN* 1.3 65.4 + - - +
30H ASP 3.8 16.4 - - - +
33H VAL* 3.7 20.2 - - + -
35H LEU* 3.7 33.9 - - + -
43H LEU* 5.6 7.9 - - + -
71H LEU* 3.7 24.9 - - + -
94H SER* 6.3 1.1 - - - -
98H LYS* 5.9 3.4 - - + -
99H LYS 4.8 4.9 - - - -
100H CYS* 3.6 32.5 - - + -
195J LEU* 4.2 7.5 - - - +
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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