Contacts of the strand formed by residues 56 - 60 (chain G) in PDB entry 1R4N
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 SER 56 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ALA 3.4 14.4 + - - -
32G HIS* 3.1 22.5 + - - +
33G VAL 2.8 23.6 + - - -
54G ILE* 3.4 7.2 + - - +
55G GLY* 1.3 74.9 - - - +
57G PHE* 1.3 63.9 + - - +
100G VAL* 4.2 3.4 - - - -
101G SER* 2.8 36.3 + - - +
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Residues in contact with PHE 57 (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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32G HIS* 3.7 3.6 + - - -
33G VAL* 3.1 13.7 - - + +
46G LEU* 3.4 40.8 - - + -
50G VAL* 3.7 24.2 - - + -
54G ILE* 5.0 3.1 - - + -
56G SER* 1.3 78.1 - - - +
58G THR* 1.3 67.9 + - - +
59G ILE* 3.8 12.8 - - + -
90G MET* 3.8 29.8 - - + -
93G LEU* 4.3 14.6 - - + -
94G GLN* 4.4 9.4 - - - -
100G VAL* 3.6 23.6 - - + -
101G SER 3.1 6.2 + - - +
102G GLY* 3.7 19.1 - - - -
103G SER* 3.1 24.1 + - - -
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Residues in contact with THR 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G HIS* 3.1 19.9 + - - -
33G VAL 3.0 6.5 + - - -
34G CYS* 3.5 6.1 - - - -
35G LEU 3.2 21.1 + - - +
57G PHE* 1.3 75.5 + - - +
59G ILE* 1.3 63.6 + - - +
60G ILE* 3.7 5.6 + - + -
103G SER* 3.2 24.3 - - - +
105G VAL* 4.0 26.5 - - + -
119G PHE* 4.7 3.4 - - + -
122G ARG* 5.7 0.3 - - - -
123G PHE* 3.6 27.0 - - + -
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Residues in contact with ILE 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.5 13.9 - - + +
36G ILE 4.3 3.6 - - - +
38G ALA* 3.9 19.3 - - + -
46G LEU* 3.6 32.8 - - + -
57G PHE* 3.8 13.9 - - + -
58G THR* 1.3 73.4 - - - +
60G ILE* 1.3 62.7 + - - +
61G ASP 3.7 1.7 + - - +
86G ALA* 3.8 29.3 - - + +
89G ALA* 4.3 4.7 - - + -
90G MET* 3.9 17.3 - - - +
93G LEU* 3.7 17.7 - - + -
103G SER 2.9 10.6 + - - +
104G PHE* 3.2 4.7 - - + +
105G VAL 2.8 25.5 + - - -
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Residues in contact with ILE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G CYS* 3.5 28.0 - - - -
35G LEU 3.1 11.3 + - - +
36G ILE* 2.5 35.7 - - + +
37G ASN* 4.1 2.8 + - - -
58G THR* 4.3 3.6 - - + -
59G ILE* 1.3 75.0 - - - +
61G ASP* 1.3 54.5 + - - +
105G VAL* 3.8 21.3 - - + -
107G GLU 3.4 17.7 - - - +
108G SER 4.3 7.9 - - - +
109G PRO* 4.5 3.2 - - + +
112G LEU* 3.7 22.9 - - + -
119G PHE* 3.5 27.1 - - + -
120G PHE* 4.0 11.2 - - + -
123G PHE* 4.7 0.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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