Contacts of the strand formed by residues 45 - 51 (chain G) in PDB entry 5DK3
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 LEU 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F TYR* 5.6 0.2 - - + -
42F GLN* 4.5 0.4 - - - +
48F PRO* 3.7 35.2 - - + -
91F TYR* 3.7 32.1 - - + -
102F PHE* 3.6 59.9 + - + +
103F GLY 5.3 0.8 + - - -
37G VAL* 4.0 14.6 - - + -
38G ARG 3.6 1.1 - - - -
39G GLN* 3.7 34.3 - - + +
44G GLY* 1.4 71.8 - - - -
46G GLU* 1.3 59.5 - - - +
95G TYR* 5.0 3.1 - - + -
110G TRP* 4.7 0.7 - - + -
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Residues in contact with GLU 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 VAL* 3.4 3.6 - - - +
38G ARG* 2.8 68.0 + - + +
44G GLY 4.0 1.5 + - - +
45G LEU* 1.3 74.1 - - - +
47G TRP* 1.3 68.9 + - - +
48G MET* 3.4 4.0 + - - +
61G ASN* 4.0 5.9 + - - +
63G LYS* 3.6 24.9 + - - +
64G PHE* 3.3 33.4 - - + -
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Residues in contact with TRP 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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98F LEU* 4.0 24.2 - - + -
99F PRO* 3.7 18.2 - - + -
100F LEU* 3.6 51.1 + - + +
101F THR* 6.0 0.4 - - - +
102F PHE* 4.4 14.4 - - + -
35G TYR* 3.2 22.7 - + + -
36G TRP 3.8 13.5 - - - -
37G VAL* 4.3 13.2 - - + -
45G LEU 4.2 1.4 + - - -
46G GLU* 1.3 72.0 - - - +
48G MET* 1.3 57.7 + - - +
49G GLY* 3.2 29.3 + - - -
50G GLY 4.1 1.3 - - - -
59G ASN* 4.0 8.1 - - + -
60G PHE* 3.5 26.2 - - - -
61G ASN* 3.0 49.3 + - + -
107G PHE* 4.4 4.7 - + - -
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Residues in contact with MET 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 32.5 + - + +
37G VAL 4.6 0.2 - - - -
38G ARG* 4.1 13.0 - - + +
46G GLU 3.8 11.2 - - - +
47G TRP* 1.3 73.8 - - - +
49G GLY* 1.3 58.1 + - - +
60G PHE* 3.7 9.5 - - - -
61G ASN* 3.0 26.3 + - - +
64G PHE* 3.7 36.2 - - + +
68G VAL* 3.8 29.8 - - + -
81G MET* 3.9 16.2 - - + +
83G LEU* 4.5 5.2 - - + -
94G TYR* 3.5 39.9 - - + -
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Residues in contact with GLY 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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35G TYR* 3.3 0.5 - - - -
36G TRP* 2.9 25.8 + - - +
47G TRP* 3.2 22.8 + - - -
48G MET* 1.3 82.0 - - - +
50G GLY* 1.3 58.3 + - - -
59G ASN 3.2 13.9 - - - -
60G PHE* 4.0 7.9 - - - -
70G LEU* 3.8 8.5 - - - -
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Residues in contact with GLY 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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33G TYR* 5.4 2.0 - - - -
34G MET 3.4 4.5 - - - -
35G TYR* 3.3 24.9 - - - -
47G TRP* 4.1 1.0 - - - -
49G GLY* 1.3 72.3 - - - -
51G ILE* 1.3 60.5 + - - -
57G GLY 4.6 0.4 - - - -
58G THR* 3.3 5.4 - - - -
59G ASN* 2.8 34.0 + - - +
70G LEU* 3.4 11.7 - - - +
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Residues in contact with ILE 51 (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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33G TYR* 3.5 9.5 - - - -
34G MET* 2.9 51.9 + - + +
36G TRP* 5.1 4.7 - - - +
50G GLY* 1.3 73.6 - - - +
52G ASN* 1.3 70.6 + - - +
53G PRO* 3.5 2.3 - - + +
56G GLY* 4.0 16.4 - - - +
57G GLY 3.6 4.5 - - - -
58G THR* 3.7 17.5 - - + -
70G LEU* 3.5 38.4 - - + +
71G THR* 4.0 15.5 - - - +
72G THR* 4.0 20.9 - - - +
79G ALA* 5.2 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