Contacts of the strand formed by residues 45 - 50 (chain G) in PDB entry 1XIW
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 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G TYR* 4.1 16.2 - - + -
38G GLN 3.3 7.4 - - - +
39G GLN* 3.7 23.1 - - + +
43G GLY 3.6 11.9 - - - +
44G THR* 1.3 79.0 - - - +
46G LYS* 1.3 71.2 + - - +
88G PHE* 6.2 1.8 - - + -
45H LEU* 6.2 3.8 - - + -
95H TYR* 4.1 12.4 - - + -
112H TRP* 3.5 69.9 + - + +
113H GLY 5.2 1.2 + - - -
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Residues in contact with LYS 46 (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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37G TYR* 3.3 8.2 - - - -
38G GLN* 2.9 53.8 + - + +
40G LYS* 4.7 17.6 - - + +
44G THR* 5.4 10.1 - - - -
45G VAL* 1.3 80.7 - - - +
47G LEU* 1.3 67.5 + - - +
48G LEU* 5.5 2.5 - - + -
110H ASP 5.9 0.4 - - - -
112H TRP* 4.8 1.6 - - - -
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Residues in contact with LEU 47 (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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35G ASN* 4.3 4.7 - - + -
36G TRP 3.6 2.9 - - - +
37G TYR* 3.5 31.7 - - + +
46G LYS* 1.3 77.3 - - - +
48G LEU* 1.3 63.5 + - - +
49G ILE 3.5 26.0 - - - +
50G TYR* 4.5 5.8 - - + -
56G HIS* 3.4 53.5 - - + +
59G VAL* 3.6 7.1 - - - +
108H TYR* 3.5 31.9 - - + -
109H PHE 3.5 20.0 + - - +
110H ASP* 4.0 10.0 + - - +
112H TRP* 4.8 2.2 - - - +
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Residues in contact with LEU 48 (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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36G TRP* 2.8 18.6 + - + +
37G TYR 4.0 3.6 - - - -
38G GLN* 3.8 28.9 - - + +
46G LYS* 4.8 3.6 - - + +
47G LEU* 1.3 78.2 - - - +
49G ILE* 1.3 71.1 + - + +
55G LEU* 3.8 0.3 - - - -
56G HIS* 3.1 24.3 + - - -
59G VAL* 3.5 29.9 - - + +
63G PHE* 4.1 28.7 - - + -
74G LEU* 4.2 9.6 - - + -
87G TYR* 3.6 36.1 - - + -
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Residues in contact with ILE 49 (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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34G LEU 5.0 0.2 - - - +
35G ASN* 3.2 4.7 - - - +
36G TRP* 2.8 38.7 + - + -
47G LEU* 3.5 5.4 - - - +
48G LEU* 1.3 88.6 - - + +
50G TYR* 1.3 65.2 + - - +
52G THR* 3.4 32.1 - - - +
53G SER* 3.7 4.9 - - - -
54G ARG 3.2 13.0 - - - +
55G LEU* 4.4 12.8 - - + -
56G HIS 4.6 0.7 - - - +
63G PHE* 4.0 7.9 - - + +
64G SER* 3.4 42.2 - - - +
65G GLY* 3.6 1.8 - - - +
74G LEU* 3.7 17.0 - - + -
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Residues in contact with TYR 50 (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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8B LEU* 3.4 25.3 + - + +
9B GLU* 3.0 39.0 - - + +
13B PHE* 5.0 0.9 - - - -
34G LEU 4.1 0.7 - - - -
35G ASN* 3.1 16.4 - - + +
47G LEU* 4.5 5.8 - - + -
49G ILE* 1.3 74.7 - - - +
51G TYR* 1.3 74.6 + - + +
52G THR 3.3 2.5 - - - -
54G ARG* 2.8 67.8 + - + +
55G LEU 4.0 9.8 + - - -
56G HIS* 4.4 5.8 - - - -
107H TRP* 4.0 7.9 - + - -
108H TYR* 3.4 51.3 + + + -
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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