Contacts of the strand formed by residues 30 - 37 (chain D) in PDB entry 5XAC
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 LYS 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ILE* 5.0 3.4 - - + +
24D ARG* 3.1 18.4 + - - -
27D HIS* 3.2 42.2 + - + +
28D PRO 3.4 0.8 - - - -
29D THR* 1.3 94.7 + - - +
31D ILE* 1.3 60.1 + - - +
32D PRO* 3.8 5.4 - - - +
53D LEU* 3.9 31.8 - - + +
54D VAL 3.3 17.5 - - - +
55D PRO* 3.8 20.4 - - - -
56D ASP* 3.1 5.8 + - - -
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 4.2 8.3 - - - +
30D LYS* 1.3 76.1 - - - +
32D PRO* 1.3 64.0 - - + +
33D VAL* 3.4 24.4 + - + +
53D LEU* 3.5 2.9 - - - -
54D VAL* 2.6 42.4 + - + +
56D ASP* 3.5 23.1 - - + +
95D ILE* 4.2 24.0 - - + -
96D SER* 4.7 7.2 - - - -
99D TYR* 3.6 51.6 - - + -
109D LEU* 4.4 5.2 - - + -
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Residues in contact with PRO 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 4.6 10.1 - - + -
23D ILE* 4.2 25.6 - - + -
24D ARG* 5.5 2.9 - - - +
30D LYS 3.8 7.4 - - - +
31D ILE* 1.3 86.0 - - + +
33D VAL* 1.3 58.7 + - - +
52D PHE 3.6 6.7 - - - +
53D LEU* 4.2 4.0 - - + -
99D TYR* 4.0 15.0 - - + +
107D GLY 3.9 16.8 - - - +
108D PHE* 3.7 29.6 - - + -
109D LEU* 3.1 26.0 + - - +
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.6 26.0 - - + +
32D PRO* 1.3 77.9 - - - +
34D ILE* 1.3 66.2 + - - +
35D ILE* 3.6 26.9 - - + -
50D THR 3.8 0.3 - - - +
52D PHE* 2.9 40.1 + - + +
54D VAL* 3.7 21.8 - - + -
63D LEU* 4.6 3.8 - - + -
95D ILE* 5.0 2.0 - - + -
109D LEU* 3.3 19.5 - - + +
111D MET* 4.0 23.6 - - + -
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Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.8 60.6 - - + -
33D VAL* 1.3 79.9 - - - +
35D ILE* 1.3 60.2 + - - +
36D GLU* 3.9 20.4 - - + +
50D THR* 3.4 7.9 - - - +
51D LYS* 4.2 16.8 - - + -
52D PHE 5.8 0.2 - - - +
108D PHE* 4.0 23.1 - - + -
109D LEU 2.8 8.3 + - - +
110D TYR* 3.5 22.2 - - + -
111D MET* 2.8 33.0 + - - +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 3.6 22.7 - - + -
34D ILE* 1.3 77.2 - - - +
36D GLU* 1.3 61.4 + - - +
47D LEU* 5.9 1.1 - - + -
49D LYS 4.4 1.9 - - - +
50D THR* 2.8 34.2 + - - +
52D PHE* 3.8 29.4 - - + -
63D LEU* 4.1 18.6 - - + -
67D ILE* 3.9 29.8 - - + -
81D LEU* 4.0 17.9 - - + -
111D MET* 3.4 11.9 - - + +
113D TYR* 4.0 23.7 - - + -
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Residues in contact with GLU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D THR* 3.6 21.8 - - - +
7D PHE* 3.0 29.9 + - - +
34D ILE* 3.9 18.6 - - + +
35D ILE* 1.3 79.8 - - - +
37D ARG* 1.3 64.9 + - - +
39D LYS* 4.8 6.9 + - - +
50D THR* 4.1 21.2 + - + +
110D TYR* 4.8 7.8 - - - -
111D MET 3.1 10.8 + - - +
112D VAL* 3.0 9.9 - - + -
113D TYR* 2.9 31.7 + - - -
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Residues in contact with ARG 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 4.2 15.2 + - - +
36D GLU* 1.3 77.4 - - - +
38D TYR* 1.3 71.7 + - - +
39D LYS* 3.3 16.0 + - - +
41D GLU* 3.6 39.0 + - + +
44D LEU 2.8 37.4 + - - -
45D PRO* 3.6 15.9 - - - +
46D VAL* 3.3 33.0 - - + +
112D VAL* 3.4 5.5 - - - +
113D TYR* 3.6 31.8 - - + +
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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