Contacts of the strand formed by residues 123 - 129 (chain G) in PDB entry 6AHU
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 ARG 123 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A A 4.4 35.2 + - - +
541B LEU* 4.0 5.8 - - - +
10G ALA* 4.7 14.8 - - - +
107G LEU 4.2 0.2 - - - +
108G VAL* 4.0 6.1 - - - +
109G ASP* 3.2 40.4 + - + +
111G LEU* 3.6 27.8 - - + +
121G LEU* 3.5 29.2 + - + +
122G THR* 1.3 76.4 - - - +
124G ILE* 1.3 64.0 + - - +
125G ARG* 4.9 9.4 - - + +
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Residues in contact with ILE 124 (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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537B ARG* 4.9 9.4 - - + -
541B LEU* 3.8 34.8 - - + -
106G GLU* 3.5 24.9 - - - +
107G LEU 4.4 2.7 - - - +
108G VAL* 5.1 3.4 - - + -
122G THR 4.0 1.0 + - - +
123G ARG* 1.3 76.8 - - - +
125G ARG* 1.3 72.1 + - - +
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Residues in contact with ARG 125 (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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35A A 2.7 62.5 + - - +
36A G 4.3 14.1 - - - -
37A C 5.0 7.8 + - + +
38A U 4.8 14.1 + - - +
106G GLU* 3.7 6.7 - - - +
107G LEU* 2.8 68.6 + - + +
109G ASP* 3.6 14.1 + - - +
123G ARG* 4.9 12.0 - - + +
124G ILE* 1.3 82.1 + - - +
126G ASN* 1.3 71.1 + - - +
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Residues in contact with ASN 126 (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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37A C 2.6 73.3 + - - +
86F ARG* 6.2 2.4 - - - +
104G THR* 3.9 20.4 - - + +
105G VAL 3.4 10.1 - - - +
106G GLU* 4.5 10.6 + - - +
107G LEU* 4.6 1.6 - - - +
125G ARG* 1.3 85.1 - - - +
127G ASN* 1.3 63.4 + - - +
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Residues in contact with ASN 127 (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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33A C 4.4 15.6 + - - -
37A C 3.4 27.0 + - - -
79F THR* 5.5 0.3 - - - +
74G LEU* 3.9 18.1 - - + +
75G GLY* 3.3 35.1 - - - +
105G VAL* 2.9 37.2 + - + +
107G LEU* 4.3 20.2 - - + +
126G ASN* 1.3 75.6 - - - +
128G SER* 1.3 77.3 + - - +
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Residues in contact with SER 128 (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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37A C 3.4 17.7 - - - +
75F THR 4.3 1.2 + - - -
78F VAL* 3.8 19.8 - - - +
79F THR* 3.4 27.9 - - - +
82F GLU* 5.5 0.7 - - - -
74G LEU* 3.5 4.3 - - - -
75G GLY* 3.3 24.8 + - - -
78G ILE* 3.8 17.5 - - - +
103G SER 4.0 3.4 - - - -
127G ASN* 1.3 85.0 + - - +
129G ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 129 (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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32A A 4.3 9.9 - - + +
78F VAL* 4.3 4.5 - - - +
73G GLY 3.4 16.4 - - - +
74G LEU* 4.5 1.3 - - + -
78G ILE* 4.5 3.4 - - - -
102G THR* 3.4 25.1 - - - +
103G SER* 3.5 15.8 + - - +
105G VAL* 3.8 26.0 - - + -
127G ASN 3.9 0.4 + - - -
128G SER* 1.3 74.1 - - - +
130G ILE* 1.3 64.8 + - - +
131G HIS* 5.2 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