Contacts of the strand formed by residues 104 - 109 (chain G) in PDB entry 5IY8
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 MET 104 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G PHE* 3.4 24.7 - - + -
77G PHE* 3.9 14.4 - - + -
79G PRO* 3.7 31.6 - - + -
100G GLU* 3.5 7.2 - - - +
101G ILE* 2.9 72.6 + - + +
103G PRO* 1.3 81.0 - - - +
105G SER* 1.3 72.0 + - - +
106G CYS* 4.5 1.1 - - + -
147G ILE* 5.0 5.4 - - + -
157G ILE* 3.9 15.3 - - - +
158G PHE* 4.2 3.6 - - - -
159G ALA* 3.9 25.1 - - + -
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Residues in contact with SER 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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99G THR 4.0 6.3 - - - -
100G GLU* 4.7 8.2 + - - +
103G PRO 3.7 4.6 + - - -
104G MET* 1.3 80.7 - - - +
106G CYS* 1.3 61.9 + - - +
157G ILE 5.5 0.2 + - - -
158G PHE* 4.2 8.0 - - - +
159G ALA 3.3 22.3 + - - +
142Q ASN* 3.6 34.4 + - - +
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Residues in contact with CYS 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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98G PHE 3.9 0.2 - - - -
99G THR* 2.8 52.7 + - - +
101G ILE* 3.5 17.7 - - + -
104G MET* 4.5 1.8 - - + -
105G SER* 1.3 77.1 - - - +
107G PHE* 1.3 59.0 + - - +
145G LEU* 3.9 25.6 - - - -
147G ILE* 5.2 1.6 - - - -
159G ALA* 3.2 18.2 - - - -
160G ILE 3.7 3.1 - - - -
161G GLY* 3.4 27.8 - - - -
142Q ASN* 3.2 4.9 - - - +
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Residues in contact with PHE 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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93G ASN* 6.1 0.2 - - + -
95G VAL 3.9 0.9 - - - -
96G GLY* 3.5 21.1 - - - -
97G LEU 3.3 28.0 - - - -
98G PHE* 3.5 26.7 - + - -
106G CYS* 1.3 72.6 - - - +
108G ILE* 1.3 60.4 + - - +
109G SER* 3.5 22.1 + - - -
159G ALA 3.3 4.2 + - - -
160G ILE* 3.6 7.5 - - + +
161G GLY 3.1 20.3 + - - +
127Q PHE* 3.2 34.1 - + - -
138Q ASP* 3.4 34.6 - - + +
141Q ALA* 3.9 3.1 - - + -
142Q ASN* 3.2 27.5 - - - +
152Q PHE* 4.0 8.3 - + - -
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Residues in contact with ILE 108 (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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96G GLY* 3.5 0.2 - - - -
97G LEU* 2.7 49.4 + - + +
99G THR* 3.6 28.3 - - + -
107G PHE* 1.3 75.5 - - - +
109G SER* 1.3 71.2 + - - +
112G SER* 4.4 1.1 - - - -
113G ILE* 3.8 8.4 - - + +
143G ILE* 3.7 14.6 - - + -
145G LEU* 3.7 26.2 - - + -
161G GLY 3.7 24.0 - - - +
162G SER* 4.2 4.9 - - - -
163G LEU* 3.7 26.2 - - + +
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Residues in contact with SER 109 (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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95G VAL 4.2 3.8 + - - -
107G PHE* 3.5 23.4 + - - -
108G ILE* 1.3 75.4 - - - +
110G ARG* 1.3 57.6 + - - +
111G HIS* 3.1 31.5 + - - +
112G SER* 2.8 26.9 + - - -
113G ILE* 3.2 9.6 + - - +
161G GLY 4.5 3.2 + - - -
125Q ALA* 3.6 27.4 - - - +
127Q PHE* 5.4 2.5 - - - -
138Q ASP* 5.0 0.8 - - - +
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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