Contacts of the strand formed by residues 30 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ILE* 5.2 1.6 - - - +
24A ARG* 3.7 19.4 + - - -
27A HIS* 3.1 52.0 + - + +
28A PRO 3.3 0.7 - - - +
29A THR* 1.3 93.8 - - - +
31A ILE* 1.3 66.0 + - - +
32A PRO* 4.1 2.6 - - - +
53A LEU* 3.7 31.0 - - + +
54A VAL 3.3 8.5 - - - +
55A PRO* 4.4 12.6 - - + -
56A ASP* 3.9 0.6 - - - +
-1B THR* 3.0 36.9 + - + +
45B PRO* 5.1 11.4 - - - -
28C PRO* 6.1 2.6 - - - +
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Residues in contact with ILE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.9 9.4 - - - +
30A LYS* 1.3 76.4 - - - +
32A PRO* 1.3 68.2 - - - +
33A VAL* 3.5 21.5 + - + +
53A LEU* 3.5 4.9 - - - -
54A VAL 2.8 34.8 + - - +
56A ASP* 3.4 22.9 - - - +
95A ILE* 4.0 24.7 - - + -
96A SER* 4.0 13.0 - - - +
99A TYR* 3.5 52.5 - - + -
109A LEU* 4.2 7.0 - - + -
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Residues in contact with PRO 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.3 15.0 - - + -
23A ILE* 4.2 12.3 - - + -
24A ARG* 4.2 11.9 - - - +
30A LYS 4.1 5.8 - - - +
31A ILE* 1.3 86.9 - - + +
33A VAL* 1.3 59.7 + - - +
52A PHE 3.5 6.7 - - - +
53A LEU* 4.1 2.4 - - + -
99A TYR* 3.9 13.9 - - + +
107A GLY 3.7 18.2 - - - +
108A PHE* 3.8 22.1 - - + -
109A LEU* 3.0 26.9 + - - +
-3B PHE* 4.2 8.5 - - + -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.6 17.3 - - + +
32A PRO* 1.3 78.4 - - - +
34A ILE* 1.3 66.4 + - - +
35A ILE* 3.7 22.2 - - + -
50A THR 3.6 1.2 - - - +
51A LYS* 3.7 2.1 - - - -
52A PHE* 2.8 40.5 + - + +
54A VAL* 3.8 22.0 - - + -
63A LEU* 5.1 0.4 - - + -
95A ILE* 3.8 19.1 - - + -
108A PHE* 4.5 0.6 - - - -
109A LEU* 3.3 15.5 - - + +
111A MET* 3.7 24.7 - - + -
-3B PHE* 5.2 0.2 - - - -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 30.5 - - + -
33A VAL* 1.3 77.2 - - - +
35A ILE* 1.3 60.3 + - - +
36A GLU* 4.0 15.0 - - + +
50A THR* 3.4 19.5 - - + +
51A LYS* 3.9 18.4 - - + -
108A PHE* 3.7 32.8 - - + -
109A LEU 2.9 7.1 + - - +
110A TYR* 3.7 39.0 - - + -
111A MET* 2.8 33.4 + - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.7 20.2 - - + -
34A ILE* 1.3 77.9 - - - +
36A GLU* 1.3 68.0 + - - +
47A LEU* 3.7 18.9 - - + +
49A LYS 4.0 4.5 - - - +
50A THR* 3.0 25.3 + - - +
52A PHE* 3.7 28.9 - - + -
54A VAL* 5.9 0.2 - - + -
63A LEU* 4.7 13.2 - - + -
67A ILE* 3.8 28.9 - - + -
81A LEU* 4.1 16.6 - - + -
111A MET* 3.4 10.1 - - + +
113A TYR* 3.9 17.0 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 3.5 17.9 - - - +
7A PHE* 2.8 33.4 + - - +
8A LYS 5.5 0.2 + - - -
10A ARG* 4.5 3.6 + - - -
34A ILE* 4.0 22.8 - - + +
35A ILE* 1.3 78.6 - - - +
37A ARG* 1.3 65.4 + - - +
47A LEU* 6.3 0.2 - - - -
50A THR* 4.0 8.8 - - + +
110A TYR* 4.6 8.5 - - - -
111A MET 3.1 10.8 + - - +
112A VAL* 3.1 16.9 - - + +
113A TYR* 3.0 31.5 + - - -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLU* 5.5 4.4 + - - -
36A GLU* 1.3 79.0 - - - +
38A TYR* 1.3 75.8 + - - +
39A LYS* 3.4 3.5 + - - -
41A GLU* 3.6 26.8 + - + +
44A LEU 2.8 29.5 + - - -
45A PRO* 3.6 13.1 - - - +
46A VAL* 3.3 35.1 - - + +
112A VAL* 4.2 2.2 - - - +
113A TYR* 3.5 30.6 - - + +
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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