Contacts of the strand formed by residues 7 - 12 (chain E) in PDB entry 1A9B
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 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D GLU* 3.3 27.4 + - - +
5E THR* 4.4 6.5 - - + +
6E PRO* 1.3 76.1 - - - +
8E ILE* 1.3 61.2 + - - +
27E TYR 3.6 1.0 - - - +
28E VAL* 3.1 7.3 - - - -
29E SER* 2.7 74.1 + - - +
30E GLY* 3.4 13.5 - - - +
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PRO* 3.9 9.8 + - + +
7E LYS* 1.3 80.1 - - - +
9E GLN* 1.3 74.2 + - - +
10E VAL* 4.1 12.6 - - + -
26E CYS* 3.6 29.2 - - - -
27E TYR 3.4 5.2 - - - +
28E VAL* 4.2 3.8 - - + -
81E CYS* 4.5 1.3 - - - +
83E VAL* 3.7 34.5 - - + -
88E LEU* 5.9 0.2 - - + -
92E LYS* 4.0 31.6 - - + +
94E VAL* 4.3 27.6 - - + +
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Residues in contact with GLN 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D VAL* 3.4 26.7 - - - +
232D GLU* 3.1 51.8 + - + +
234D ARG* 3.3 32.9 + - - +
8E ILE* 1.3 82.9 - - - +
10E VAL* 1.3 62.0 + - - +
11E TYR* 3.2 18.6 - - + -
26E CYS* 3.4 0.2 - - - -
27E TYR* 2.9 35.8 + - + +
94E VAL* 5.4 1.6 - - - -
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ARG* 5.4 0.4 - - - -
8E ILE* 4.1 4.5 - - + -
9E GLN* 1.3 72.8 - - - +
11E TYR* 1.3 63.4 + - - +
24E LEU* 4.1 14.8 - - + -
25E ASN 3.2 10.1 - - - +
26E CYS* 4.1 1.8 - - + -
40E LEU* 5.3 0.7 - - + -
80E ALA 4.7 2.9 - - - +
81E CYS* 3.4 37.2 - - + +
94E VAL* 3.5 32.8 - - + +
95E LYS 4.5 1.1 - - - +
96E TRP* 3.4 43.0 - - + +
97E ASP 4.4 2.3 + - - -
100E MET 4.8 6.9 - - - -
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Residues in contact with TYR 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 3.2 58.3 - - + +
235D PRO* 2.7 31.0 + - - +
242D GLN* 3.3 21.1 - - - -
9E GLN* 3.2 21.8 - - + -
10E VAL* 1.3 74.6 - - - +
12E SER* 1.3 61.2 + - - +
24E LEU* 3.6 8.7 - - - +
25E ASN* 2.7 59.0 + - + +
27E TYR* 3.4 25.4 - - + +
66E LEU* 3.5 7.6 - - - +
96E TRP* 3.7 11.7 - - - +
100E MET 4.4 5.4 - - - +
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Residues in contact with SER 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 5.5 0.3 - - - +
242D GLN* 2.8 21.1 + - - +
11E TYR* 1.3 77.6 - - - +
13E ARG* 1.3 63.0 + - - +
14E HIS* 3.1 14.2 + - - +
15E PRO* 4.7 1.0 - - - +
16E ALA* 4.2 7.6 + - - +
22E ASN* 3.6 13.0 - - - -
23E PHE 3.0 12.1 - - - -
25E ASN* 3.7 4.5 - - - -
71E PHE* 4.0 18.4 - - - -
96E TRP* 4.1 12.3 + - - +
98E ARG 5.2 3.3 + - - -
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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