Contacts of the strand formed by residues 126 - 131 (chain G) in PDB entry 6CP3
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 ILE 126 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ILE* 3.5 26.0 - - + +
109G THR* 4.8 9.0 - - + +
115G LYS* 4.3 7.4 - - + +
118G LEU* 3.7 15.9 - - + -
119G LEU* 3.5 43.1 - - + +
122G HIS 3.9 8.7 + - - +
123G PRO 4.5 5.1 + - - +
124G ASN 3.5 1.1 - - - +
125G ASN* 1.3 77.5 - - + +
127G LYS* 1.3 62.4 + - - +
128G LEU 4.1 4.7 - - - +
129G SER* 3.6 24.5 - - - +
47I TYR* 3.4 29.7 - - + +
48I LYS 3.5 13.7 - - - +
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Residues in contact with LYS 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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106G ASP* 3.3 37.5 + - - +
107G ILE 3.2 7.7 + - - +
124G ASN 5.1 3.1 - - - +
125G ASN 3.6 8.3 - - - +
126G ILE* 1.3 77.7 - - - +
128G LEU* 1.3 60.0 + - - +
154G MET* 3.8 28.5 + - + +
159G TYR* 4.4 5.1 + - - -
46I GLN* 3.3 19.5 - - + +
47I TYR* 2.9 34.6 + - - +
48I LYS* 5.4 4.7 - - - +
49I ASN* 5.6 1.1 - - - +
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Residues in contact with LEU 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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107G ILE 4.0 3.6 + - - +
108G VAL* 3.3 47.9 - - + +
109G THR 3.3 2.8 + - - -
126G ILE* 3.9 1.8 - - - +
127G LYS* 1.3 79.3 - - - +
129G SER* 1.3 73.3 + - - +
130G ILE* 4.6 13.2 - - + -
146G ILE* 6.0 0.7 - - + -
149G LYS* 4.6 11.0 - - + +
150G LEU* 4.5 8.3 - - + -
153G VAL* 4.6 13.0 - - + -
154G MET* 3.8 25.4 - - + -
44I TYR* 4.1 21.8 - - + -
45I THR 3.8 4.9 - - - -
46I GLN* 3.8 29.4 - - + +
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Residues in contact with SER 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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109G THR* 3.3 18.5 + - - -
111G GLY 6.0 0.2 - - - -
115G LYS* 3.5 29.7 - - - +
126G ILE* 3.6 13.9 - - - +
128G LEU* 1.3 79.1 + - - +
130G ILE* 1.3 66.1 + - - +
131G ASN* 3.8 2.5 + - - +
43I PHE 3.6 0.9 - - - +
44I TYR* 3.3 3.2 - - - -
45I THR* 3.0 38.0 + - - -
47I TYR* 3.9 6.3 - - - -
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Residues in contact with ILE 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G VAL* 4.9 7.0 - - + -
109G THR 3.0 6.5 + - - +
110G ILE* 3.7 26.9 - - + -
111G GLY* 3.1 26.9 + - - +
128G LEU* 4.6 10.8 - - + -
129G SER* 1.3 75.6 - - - +
131G ASN* 1.3 63.8 + - - +
133G ILE* 3.8 19.5 - - + +
146G ILE* 3.7 44.9 - - + -
149G LYS* 5.5 4.3 - - + -
42I ALA* 4.2 8.7 - - + -
43I PHE 3.3 4.3 - - - +
44I TYR* 3.7 25.4 - - + -
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Residues in contact with ASN 131 (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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411C ASP* 5.7 1.6 + - - -
80G ASP* 2.9 23.4 - - - +
112G ASP* 4.2 21.6 + - - +
115G LYS* 5.5 6.2 - - - +
129G SER* 4.9 2.9 - - - +
130G ILE* 1.3 76.0 - - - +
132G GLY* 1.3 73.7 + - - +
133G ILE* 3.9 2.9 - - - -
42I ALA* 3.3 3.5 - - - +
43I PHE* 2.5 55.9 + - + +
45I THR* 6.1 1.1 - - - +
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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