Contacts of the strand formed by residues 11 - 17 (chain S) 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 VAL 11 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9S GLN 3.5 10.8 + - - +
10S ASN* 1.3 86.5 + - - +
12S THR* 1.3 65.8 + - - +
13S GLU* 5.7 1.1 - - + -
44T ARG* 4.0 29.2 - - + +
45T ILE 3.8 3.6 - - - +
46T ALA* 4.6 12.3 - - + -
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Residues in contact with THR 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S ASN* 3.6 20.4 + - - -
11S VAL* 1.3 80.9 + - - +
13S GLU* 1.3 63.6 + - - +
14S TYR* 3.5 41.3 - - + +
43T LEU 3.8 0.3 - - - +
44T ARG* 3.1 8.3 - - - +
45T ILE* 2.9 47.5 + - + +
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Residues in contact with GLU 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S VAL* 5.7 1.3 - - + -
12S THR* 1.3 77.7 - - - +
14S TYR* 1.3 78.2 + - - +
133S GLY 4.7 0.3 - - - +
42T LYS* 3.2 53.8 + - + +
43T LEU 3.2 13.9 - - - +
44T ARG* 4.3 23.8 + - + +
57T THR* 5.5 3.8 - - - -
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Residues in contact with TYR 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S THR* 3.5 29.3 - - + +
13S GLU* 1.3 82.8 - - - +
15S VAL* 1.3 69.1 + - - +
16S VAL* 4.2 0.2 - - - +
129S GLN* 4.7 18.6 + - + -
133S GLY* 3.1 27.8 - - - +
134S ALA* 4.5 2.5 - - - -
135S PHE* 3.7 50.3 - + + +
42T LYS* 3.2 10.4 - - - +
43T LEU* 2.9 32.4 + - + +
45T ILE* 5.1 8.3 - - + -
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Residues in contact with VAL 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S TYR* 1.3 77.5 - - - +
16S VAL* 1.3 76.5 + - - +
17S ARG* 4.8 4.0 - - + +
133S GLY 4.4 1.3 + - - +
134S ALA* 3.8 20.1 - - + +
135S PHE* 2.5 35.7 + - - +
38T GLY 4.3 6.3 - - - +
39T GLU* 4.2 17.5 - - + -
41T GLY 3.9 6.3 - - - +
42T LYS* 4.2 15.9 - - + -
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Residues in contact with VAL 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14S TYR 4.2 0.2 - - - +
15S VAL* 1.3 82.1 - - - +
17S ARG* 1.3 71.2 + - - +
18S VAL* 4.5 0.7 - - + -
127S PHE* 4.1 26.9 - - + -
135S PHE* 3.2 7.2 - - + +
137S ALA* 4.4 8.5 - - + +
31T TRP* 5.1 1.8 - - + -
39T GLU* 3.1 24.9 - - - -
40T VAL* 3.2 26.5 + - + -
41T GLY 3.1 16.4 + - - +
43T LEU* 4.0 20.2 - - + +
56T PHE* 3.8 20.6 - - + -
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Residues in contact with ARG 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 4.8 6.0 - - + +
16S VAL* 1.3 73.5 - - - +
18S VAL* 1.3 66.9 + - - +
19S PRO* 3.7 8.5 - - + +
130S CYS* 3.5 22.0 - - - +
132S ASP* 2.8 29.8 + - - -
134S ALA* 3.5 20.3 - - - +
135S PHE 2.8 11.2 + - - +
136S GLU* 2.8 41.6 + - + +
137S ALA* 2.9 27.2 + - - +
38T GLY* 3.3 33.9 - - - +
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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