Contacts of the strand formed by residues 39 - 43 (chain G) in PDB entry 1A81
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 TYR 39 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G PHE* 3.2 40.8 - + - -
29G LEU* 4.2 4.5 - - - -
37G GLY 3.7 5.8 - - - +
38G LEU* 1.3 74.2 - - - +
40G LEU* 1.3 62.0 + - - +
53G LEU* 4.5 10.5 - - + -
54G SER 3.0 4.0 - - - +
55G VAL* 3.1 28.3 - - + -
89G CYS* 4.5 13.1 + - + +
90G HIS* 5.9 0.7 + - - -
93G SER* 5.2 3.8 - - - -
103G LEU* 3.4 47.0 - - + +
104G LYS 4.3 1.9 + - - -
105G LYS 2.9 13.1 + - - -
106G PRO* 3.6 27.9 - - + +
107G PHE* 2.7 28.9 + - - +
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PHE* 3.9 9.9 - - - +
17G PHE* 3.2 35.4 - - + -
20G ILE* 5.8 0.4 - - + -
25G ALA* 3.8 31.6 - - + +
28G TYR* 4.2 10.1 - - + -
29G LEU* 3.6 30.3 - - + -
39G TYR* 1.3 81.3 - - - +
41G LEU* 1.3 70.8 + - - +
42G ARG* 4.4 7.2 - - + +
52G ALA 4.0 0.2 - - - +
53G LEU* 3.8 5.3 - - - +
54G SER* 2.6 44.3 + - - +
107G PHE* 4.3 11.0 - - + +
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 4.7 3.8 - - + -
13G LEU* 4.9 6.1 - - + -
15G PHE* 3.0 30.4 + - + +
16G PHE* 2.7 51.6 - - + -
17G PHE 2.9 4.8 + - - -
40G LEU* 1.3 73.4 - - - +
42G ARG* 1.3 61.9 + - - +
51G PHE* 3.7 30.5 - - + -
52G ALA 2.4 42.8 - - - +
53G LEU* 4.0 14.4 - - + +
66G ILE* 4.2 7.6 - - + -
85G PRO* 4.4 15.3 - - + -
89G CYS* 5.0 5.4 - - - -
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Residues in contact with ARG 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G PHE* 3.3 10.1 - - - -
17G PHE 3.9 6.7 - - - +
18G GLY 3.9 10.1 - - - +
20G ILE* 3.9 28.5 + - + -
22G ARG* 3.6 17.2 - - - +
25G ALA* 4.0 6.5 - - - +
40G LEU* 4.6 10.3 - - + +
41G LEU* 1.3 74.9 - - - +
43G GLN* 1.3 64.7 + - - +
44G SER* 6.1 0.2 - - - +
45G ARG* 5.3 0.6 - - - +
51G PHE* 3.2 6.1 - - - +
52G ALA* 2.8 52.0 + - + +
54G SER* 3.2 11.0 + - - +
63G HIS* 2.4 50.3 + - - +
181H PTR 2.8 38.2 + - - -
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Residues in contact with GLN 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G PHE* 3.0 24.7 - - + -
18G GLY* 3.1 16.6 + - - +
19G ASN* 3.9 34.5 + - + +
20G ILE 4.8 1.9 + - - +
42G ARG* 1.3 87.8 + - - +
44G SER* 1.3 75.3 + - - +
45G ARG* 3.9 4.9 + - - +
50G GLY 4.6 4.3 - - - +
51G PHE* 3.9 8.9 - - + -
52G ALA* 4.5 0.6 - - - +
116G LYS 5.7 0.6 + - - -
117G THR* 5.9 1.6 - - - +
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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