Contacts of the strand formed by residues 103 - 107 (chain G) in PDB entry 5M64
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 103 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1659A LYS* 3.0 30.0 - - - +
1660A VAL* 3.3 23.5 + - + -
1662A ASN 3.2 20.6 + - - +
1663A ALA* 3.2 29.9 + - - -
57G PRO* 4.3 14.4 - - + +
58G LEU* 4.6 9.7 - - - +
89G ILE* 3.4 40.8 - - + +
91G ASP* 3.2 21.5 - - - +
101G SER 3.5 2.2 + - - +
102G GLU* 1.3 76.2 - - - +
104G LEU* 1.3 66.7 + - - +
105G ILE* 4.1 15.0 - - + -
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Residues in contact with LEU 104 (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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1657A LEU* 3.8 29.2 - - + -
1658A ALA 3.2 8.3 - - - +
1659A LYS* 4.1 23.1 - - + -
133F VAL* 5.2 0.2 - - + -
135F ARG* 4.0 1.1 - - - +
145F ASP* 3.4 15.3 - - - +
90G LEU 4.6 0.2 - - - +
91G ASP* 3.9 14.1 + - + +
92G ALA* 3.4 29.8 + - + +
93G ASP* 3.3 39.9 - - - +
102G GLU* 5.6 1.3 - - - +
103G LYS* 1.3 76.6 - - - +
105G ILE* 1.3 71.4 + - - +
106G LYS 4.4 0.2 + - - -
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Residues in contact with ILE 105 (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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1657A LEU* 3.3 3.2 - - - -
1658A ALA* 3.0 37.0 + - + +
1660A VAL* 5.6 2.9 - - + -
49G LEU* 3.8 26.5 - - + -
54G LEU* 6.5 0.9 - - + -
57G PRO* 5.5 5.8 - - + -
89G ILE* 3.7 17.5 - - + -
90G LEU 4.4 7.0 - - - +
103G LYS* 4.1 16.6 - - + -
104G LEU* 1.3 84.8 - - - +
106G LYS* 1.3 70.5 + - - +
107G ILE* 3.1 4.0 + - - +
114G GLY* 4.1 5.2 - - - -
115G PHE 3.6 19.1 - - - +
116G THR* 3.4 24.7 - - - +
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Residues in contact with LYS 106 (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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10A GLU* 4.3 12.3 + - - -
1655A ASP* 3.8 27.6 - - + +
1656A VAL 3.6 11.7 - - - +
1657A LEU* 3.6 11.9 - - + +
137F TYR* 5.5 1.6 - - - +
92G ALA* 5.4 10.2 - - + +
104G LEU 4.3 0.4 + - - -
105G ILE* 1.3 71.1 - - - +
107G ILE* 1.3 65.8 + - - +
108G THR* 3.9 3.3 + - - +
115G PHE* 2.9 61.5 + - - +
117G TRP* 5.7 11.3 - - - -
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Residues in contact with ILE 107 (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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1655A ASP* 5.5 0.3 - - - +
1656A VAL* 3.0 46.7 + - + +
1657A LEU* 4.3 6.3 - - - +
1658A ALA* 5.2 6.1 - - + -
92F ARG* 6.1 0.2 - - - +
96F THR* 3.9 24.5 - - + -
99F LEU* 4.8 2.0 - - + -
100F GLN* 5.4 8.1 - - + -
132F LEU* 4.6 5.8 - - + -
105G ILE 3.1 5.5 + - - +
106G LYS* 1.3 78.9 - - - +
108G THR* 1.3 73.5 - - - +
109G PRO* 3.4 8.1 - - + +
111G THR 4.1 0.2 - - - +
112G PRO* 3.4 26.5 - - + +
113G PHE 3.6 13.2 - - - +
114G GLY* 3.6 9.0 - - - +
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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