Contacts of the strand formed by residues 24 - 32 (chain A) in PDB entry 5A72
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE 3.8 0.2 + - - -
20A VAL* 3.0 25.2 + - - -
22A ALA 3.4 1.4 - - - -
23A ASP* 1.3 80.3 - - - +
25A CYS* 1.3 64.4 + - - +
47A THR 3.2 11.4 - - - -
48A VAL* 4.4 2.2 - - - -
49A PHE* 4.3 2.2 - - - -
102A LYS* 2.8 23.3 + - - -
515C G 3.5 12.6 - - - +
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Residues in contact with CYS 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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20A VAL* 4.4 4.0 - - - +
24A GLY* 1.3 76.0 - - - +
26A ILE* 1.3 61.6 + - - +
27A ASN* 3.7 25.8 - - - -
45A SER* 3.6 2.6 + - - +
46A LEU* 3.4 2.3 - - - -
47A THR* 2.8 39.2 + - - +
49A PHE* 3.7 20.9 - - + -
102A LYS* 4.5 2.2 - - - +
139A THR* 5.7 1.1 - - - -
515C G 4.0 1.1 - - + -
516C A 3.3 47.1 - - - +
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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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20A VAL* 4.2 12.8 - - + -
25A CYS* 1.3 72.0 - - - +
27A ASN* 1.3 64.4 + - - +
45A SER 3.4 6.3 - - - +
46A LEU* 3.6 26.2 - - + -
92A LEU* 3.8 20.4 - - + -
99A LEU* 3.7 30.7 - - + -
102A LYS* 4.3 20.2 - - + +
105A GLN* 3.6 45.8 + - + +
106A ALA* 4.0 4.9 - - + +
109A VAL* 3.9 17.3 - - + -
135A VAL* 4.1 1.6 - - - +
139A THR* 4.6 3.3 - - - +
516C A 5.6 0.2 + - - -
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Residues in contact with ASN 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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25A CYS* 3.7 16.9 - - - -
26A ILE* 1.3 77.7 - - - +
28A ALA* 1.3 86.6 + - - +
29A GLN* 3.8 21.2 - - + +
44A VAL* 3.4 3.3 - - - -
45A SER* 2.8 43.3 + - - +
109A VAL* 3.9 9.6 - - - +
135A VAL* 3.8 10.4 - - - +
139A THR* 4.2 4.5 - - - +
144A ARG* 3.4 10.7 + - - -
516C A 3.9 11.5 - - - +
517C C 3.3 31.0 + - - -
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Residues in contact with ALA 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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27A ASN* 1.3 88.0 + - - +
29A GLN* 1.3 62.9 + - - +
42A VAL* 4.9 0.9 - - + -
43A ARG 3.1 10.1 - - - +
44A VAL* 4.2 5.8 - - + -
109A VAL* 4.4 1.8 - - + -
112A ILE* 3.7 29.8 - - + -
132A ALA* 3.7 18.0 - - + +
135A VAL* 4.0 11.6 - - + +
144A ARG* 2.9 19.9 + - - -
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Residues in contact with GLN 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 ASN* 3.8 20.3 - - - +
28A ALA* 1.3 79.4 - - - +
30A ILE* 1.3 68.5 + - - +
31A VAL* 3.7 7.8 + - + +
41A GLN 3.5 0.2 - - - +
42A VAL* 3.4 3.3 - - - -
43A ARG* 2.7 58.9 + - + +
45A SER* 4.8 10.5 + - - -
132A ALA* 4.5 2.0 - - - +
144A ARG* 3.5 11.2 - - - +
517C C 4.2 23.5 - - - +
518C G 3.3 44.2 + - - +
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Residues in contact with ILE 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 GLN* 1.3 76.1 - - - +
31A VAL* 1.3 60.2 + - - +
40A TYR* 3.6 29.2 - - + -
41A GLN 3.2 10.1 - - - +
42A VAL* 4.7 4.9 - - + -
125A LEU* 6.4 0.2 - - + -
129A ALA* 3.8 30.3 - - + +
132A ALA* 4.2 13.7 - - + -
133A ASP* 4.6 3.1 - - - +
144A ARG* 4.3 4.1 - - - +
146A ILE* 3.3 41.6 + - + +
147A LEU* 3.6 31.2 - - - +
148A ALA* 3.7 5.4 - - - +
151A VAL* 3.6 11.9 - - + -
518C G 4.2 6.3 + - - -
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Residues in contact with VAL 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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29A GLN* 4.2 10.3 - - + +
30A ILE* 1.3 75.6 - - - +
32A SER* 1.3 63.1 + - - +
33A ARG* 3.4 35.0 - - + +
40A TYR* 3.4 6.2 - - - -
41A GLN* 2.8 46.8 + - + +
43A ARG* 3.6 48.5 - - + +
146A ILE* 4.5 1.6 - - - -
518C G 5.9 0.4 - - - +
519C T 4.1 19.1 - - + -
520C T 6.5 0.4 - - + -
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Residues in contact with SER 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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30A ILE 4.0 1.4 + - - -
31A VAL* 1.3 77.6 - - - +
33A ARG* 1.3 68.3 + - - +
34A GLU* 4.5 14.7 + - - +
39A LYS 3.8 1.7 + - - -
40A TYR* 3.8 21.8 - - - -
146A ILE* 4.0 13.2 - - - +
519C T 4.5 14.5 + - - +
520C T 5.0 9.2 - - - +
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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