Contacts of the strand formed by residues 21 - 30 (chain A) in PDB entry 5CYP
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 GLY 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLN* 1.3 72.3 - - - +
22A PHE* 1.3 67.3 + - - -
23A GLU* 4.1 5.9 + - - +
80A ARG* 3.2 22.0 - - - +
82A LYS* 5.3 4.9 - - - -
127A ARG* 5.4 5.9 + - - -
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Residues in contact with PHE 22 (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 GLN* 3.9 24.2 - - + -
21A GLY* 1.3 76.3 - - - -
23A GLU* 1.3 65.8 + - - +
24A PHE* 4.9 0.7 - - - +
79A VAL* 3.5 34.8 - - + -
80A ARG 3.1 9.8 + - - +
81A MET* 3.2 11.9 - - + +
82A LYS 2.8 23.5 + - - -
127A ARG* 6.2 2.2 - - - -
270A MET* 4.9 21.7 - - + +
271A GLN* 5.1 9.4 - - - +
274A LYS* 5.3 5.6 - - + +
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Residues in contact with GLU 23 (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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21A GLY 5.0 4.5 - - - +
22A PHE* 1.3 74.0 - - - +
24A PHE* 1.3 61.4 + - - +
25A ASN* 5.3 1.6 - - - +
82A LYS* 3.9 29.7 - - + +
127A ARG* 5.7 2.6 + - - -
128A ILE 4.6 1.9 - - - +
129A PRO* 3.8 11.4 - - - +
130A ASP* 2.8 51.7 + - + +
134A HIS* 4.2 1.8 - - + -
270A MET* 4.7 1.6 - - - +
274A LYS* 2.9 38.1 + - - +
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Residues in contact with PHE 24 (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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22A PHE 3.9 2.4 + - - +
23A GLU* 1.3 76.5 - - - +
25A ASN* 1.3 62.0 + - - +
26A ILE* 3.6 29.2 - - + -
81A MET* 5.7 4.7 - - + -
82A LYS 3.5 7.0 + - - +
83A LEU* 3.6 11.9 - - + +
84A THR 2.9 25.6 + - - -
134A HIS* 3.5 29.4 - - + -
135A CYS* 4.2 9.9 - - + -
265A LEU* 3.4 26.7 - - + -
266A ILE* 3.9 17.7 - - + -
270A MET* 3.7 37.5 - - + -
273A ILE* 4.0 19.5 - - + -
274A LYS* 3.9 7.4 - - + -
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Residues in contact with ASN 25 (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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23A GLU* 5.3 1.0 - - - +
24A PHE* 1.3 80.3 + - - +
26A ILE* 1.3 63.1 + - - +
82A LYS 4.8 0.7 - - - +
84A THR* 3.2 30.2 + - - +
86A ILE* 4.5 8.7 - - + -
130A ASP 3.0 26.9 + - - +
131A THR* 3.2 12.8 - - - -
132A ARG 2.5 30.8 + - - +
133A VAL* 4.1 6.5 - - - -
134A HIS* 3.0 18.0 + - - +
135A CYS* 3.1 26.2 + - - +
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Residues in contact with ILE 26 (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 PHE* 3.6 31.4 - - + -
25A ASN* 1.3 77.4 - - - +
27A MET* 1.3 64.3 + - - +
28A VAL* 5.1 4.0 - - + +
43A LEU* 4.7 16.8 - - + -
83A LEU* 4.0 17.5 - - + -
84A THR 2.9 10.9 + - - +
85A VAL* 3.2 14.9 - - + +
86A ILE* 2.8 27.0 + - - +
135A CYS* 3.3 15.3 - - + +
137A LEU* 4.0 30.7 - - + -
265A LEU* 4.7 12.6 - - + -
266A ILE* 4.1 10.1 - - + -
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Residues in contact with MET 27 (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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26A ILE* 1.3 75.1 - - - +
28A VAL* 1.3 62.1 + - - +
29A VAL* 3.7 25.6 - - + -
67A ILE* 5.4 0.9 - - + -
86A ILE* 3.6 25.1 - - + +
88A THR* 4.2 7.2 - - + -
104A ILE* 3.9 18.4 - - + -
107A PHE* 3.4 35.9 - - + -
108A ILE* 4.3 16.2 - - + -
133A VAL* 3.7 25.4 - - + -
135A CYS 2.9 9.8 + - - +
136A CYS* 3.2 8.9 - - - -
137A LEU 2.7 32.6 + - - +
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Residues in contact with VAL 28 (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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26A ILE* 4.2 2.4 + - + -
27A MET* 1.3 73.7 - - - +
29A VAL* 1.3 57.6 + - - +
36A LYS* 4.2 11.4 - - + +
39A LEU* 5.1 2.7 - - + -
40A ILE* 3.6 26.0 - - + -
85A VAL* 4.6 6.7 - - + -
86A ILE 3.1 14.2 + - - +
87A ASP* 3.5 24.2 - - - +
88A THR* 2.5 31.1 + - - +
137A LEU* 3.7 18.6 - - + -
139A PHE* 3.8 26.5 - - + -
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Residues in contact with VAL 29 (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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27A MET* 3.7 14.4 - - + -
28A VAL* 1.3 79.6 - - - +
30A GLY* 1.3 54.6 + - - +
36A LYS* 3.5 5.6 - - - +
88A THR* 3.6 4.7 - - + +
91A PHE* 3.5 20.0 - - + -
104A ILE* 3.9 22.9 - - + -
136A CYS* 3.7 22.4 - - - -
137A LEU 2.8 12.9 + - - +
138A TYR* 3.3 24.7 - - + -
139A PHE* 2.7 34.2 + - - -
154A PHE* 4.1 5.6 - - + -
158A LEU* 4.0 8.3 - - + -
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Residues in contact with GLY 30 (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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29A VAL* 1.3 81.4 - - - +
31A GLN* 1.3 64.3 + - - -
36A LYS* 2.5 33.3 + - - +
90A GLY* 3.3 6.6 - - - -
91A PHE* 3.4 22.0 - - - -
138A TYR* 5.1 0.9 - - - -
139A PHE* 4.0 15.3 - - - -
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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