Contacts of the strand formed by residues 18 - 24 (chain C) in PDB entry 5IYB
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 ASN 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLU* 4.4 5.8 - - + +
14C LEU* 3.3 10.9 - - - +
15C THR* 2.8 43.7 + - + +
17C GLU* 1.3 82.1 - - - +
19C VAL* 1.3 60.9 + - - +
20C LYS* 5.1 2.2 - - + +
232C ASN* 3.2 28.5 + - - +
233C VAL 3.6 1.3 - - - -
234C GLU* 3.9 22.7 + - - +
241C PRO* 3.9 2.4 - - - +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.7 12.8 - - + -
13C GLU 3.5 7.0 - - - +
14C LEU* 4.3 11.0 - - + -
18C ASN* 1.3 75.7 - - - +
20C LYS* 1.3 62.1 + - - +
21C PHE* 4.0 26.5 - - + -
232C ASN* 3.3 3.3 - - - +
233C VAL* 2.9 49.4 + - + -
241C PRO* 3.6 30.3 - - + +
242C GLU* 4.8 9.0 - - - +
245C VAL* 4.5 3.1 - - + -
105K PHE* 5.1 4.3 - - + -
109K ILE* 5.1 6.7 - - + -
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 3.9 1.6 - - - +
12C THR* 2.8 33.4 + - + +
13C GLU* 2.8 57.9 + - + +
18C ASN* 5.7 1.8 - - + -
19C VAL* 1.3 73.1 - - - +
21C PHE* 1.3 63.6 + - - +
207C GLU* 3.0 22.6 + - - -
208C TYR* 3.1 29.9 - - + +
231C TYR 3.6 11.0 - - - +
232C ASN* 3.6 27.5 - - - +
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Residues in contact with PHE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.5 6.5 - - + -
10C ARG 3.2 16.2 - - - +
11C ILE* 3.6 17.5 - - + -
12C THR* 4.2 3.6 - - - +
19C VAL* 4.0 34.3 - - + -
20C LYS* 1.3 78.2 - - - +
22C ILE* 1.3 65.2 + - - +
23C ILE* 3.7 27.8 - - + -
38C PHE* 4.6 14.1 - + - -
208C TYR* 5.5 0.5 + - - -
230C TYR* 3.6 2.8 - - - +
231C TYR* 2.7 78.4 + + + +
233C VAL* 4.5 2.9 - - + -
245C VAL* 4.5 14.8 - - + -
105K PHE* 4.7 7.6 - + - -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.7 3.8 - - - +
10C ARG* 3.0 52.9 + - + +
12C THR* 4.3 15.7 - - - +
21C PHE* 1.3 80.3 - - - +
23C ILE* 1.3 60.0 + - - +
24C GLU* 4.1 13.8 + - + +
208C TYR* 5.3 4.5 - - + -
228C ARG* 3.4 31.4 - - + -
229C PHE 3.2 15.7 - - - +
230C TYR* 3.7 29.2 - - + -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO 5.4 0.4 - - - -
8C THR 3.5 11.9 - - - +
9C VAL* 4.6 7.9 - - + -
21C PHE* 3.7 29.8 - - + -
22C ILE* 1.3 74.6 - - - +
24C GLU* 1.3 65.7 + - - +
26C THR* 3.6 26.0 - - + -
31C ALA* 6.1 0.2 - - - -
34C ILE* 4.7 10.1 - - + -
228C ARG* 3.4 1.4 - - - -
229C PHE* 2.9 37.6 + - + -
231C TYR* 3.8 26.0 - - + +
101K LEU* 4.1 32.5 - - + -
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 3.7 1.9 - - - +
8C THR* 2.9 45.5 + - - +
9C VAL* 6.3 0.2 - - - -
10C ARG* 2.4 44.7 + - + +
22C ILE* 4.1 9.7 - - + +
23C ILE* 1.3 79.8 - - - +
25C ASN* 1.3 74.4 + - - +
26C THR* 3.3 3.9 + - - -
227C GLU* 3.7 8.2 - - - +
228C ARG* 2.9 37.8 + - + +
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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