Contacts of the strand formed by residues 125 - 131 (chain G) in PDB entry 1YKN
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 HIS 125 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72G GLN* 4.2 7.3 - - - +
73G ALA 4.9 1.2 + - - -
79G TYR* 3.7 3.8 + - - -
111G PRO* 3.5 18.3 - - - +
112G GLY 5.3 0.4 + - - -
114G VAL* 4.0 20.4 - - + -
122G MET* 4.0 10.1 - - + +
123G ALA 2.9 21.3 + - - +
124G PRO* 1.3 75.9 - - - +
126G ILE* 1.4 67.2 + - - +
127G ASN* 3.7 20.0 + - - -
142G ARG* 3.5 38.3 + - - -
143G LEU 3.3 11.0 - - - +
144G TYR* 4.0 15.5 - - + -
145G PHE* 4.6 0.7 - - - -
344H SER* 2.7 27.9 + - - -
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Residues in contact with ILE 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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49G ILE* 5.6 0.2 - - + -
51G LEU* 3.6 27.8 - - + -
70G VAL* 4.1 16.8 - - + -
71G TRP 4.1 4.7 - - - +
72G GLN* 3.1 31.9 - - + +
106G LEU* 5.3 0.9 - - + -
108G THR* 4.6 1.1 - - + -
109G VAL 5.1 0.2 - - - +
111G PRO* 4.2 7.4 - - + -
125G HIS* 1.4 80.2 - - - +
127G ASN* 1.3 71.6 + - - +
128G ILE* 3.6 13.9 + - + +
142G ARG* 3.4 5.0 - - - -
143G LEU* 2.9 40.6 + - + +
145G PHE* 4.1 22.0 - - + -
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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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69G GLU 3.7 0.2 - - - +
70G VAL* 3.3 6.4 - - - +
71G TRP* 2.8 57.8 + - + +
79G TYR* 3.0 25.9 + - - -
125G HIS* 3.7 7.7 + - - -
126G ILE* 1.3 68.0 - - - +
128G ILE* 1.3 62.8 + - - +
141G THR 4.0 4.3 - - - +
142G ARG* 3.5 26.3 + - - +
344H SER* 3.4 21.2 - - - -
345H GLU* 3.8 4.7 - - - +
470H ILE* 4.0 20.9 - - + +
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Residues in contact with ILE 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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68G LEU* 4.2 22.2 - - + -
69G GLU 3.5 4.7 - - - +
70G VAL* 3.9 17.3 - - + -
104G TRP* 5.2 4.7 - - + -
126G ILE* 3.6 8.7 + - + +
127G ASN* 1.3 80.5 - - - +
129G SER* 1.3 74.9 + - - +
130G LEU* 4.5 2.5 - - + +
139G LEU 3.6 0.3 - - - +
140G HIS* 3.2 7.2 + - - +
141G THR* 2.8 57.6 + - + +
143G LEU* 3.9 25.4 - - + +
185G PHE* 3.9 28.5 - - + -
187G ILE* 4.6 5.8 - - + -
470H ILE* 6.5 0.2 - - - -
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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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67G PHE 3.9 0.3 - - - +
68G LEU* 3.1 6.9 - - - +
69G GLU* 2.8 45.1 + - - -
128G ILE* 1.3 76.4 - - - +
130G LEU* 1.3 60.0 + - - +
131G PHE* 3.8 21.5 - - - -
138G HIS* 4.1 8.5 + - - -
139G LEU 3.4 5.8 - - - -
140G HIS* 3.5 23.7 + - - -
470H ILE* 5.4 9.7 + - - +
473H LYS* 5.8 2.2 - - - +
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Residues in contact with LEU 130 (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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55G VAL* 4.2 12.6 - - + -
63G VAL* 5.8 0.2 - - + -
66G SER* 3.9 30.1 - - - +
67G PHE 3.8 1.6 - - - -
68G LEU* 4.1 17.9 - - + +
128G ILE* 4.2 5.3 - - + +
129G SER* 1.3 73.6 - - - +
131G PHE* 1.3 62.2 + - - +
135G ILE* 4.0 16.5 - - + +
138G HIS* 3.4 6.4 - - - +
139G LEU* 2.9 47.1 + - + +
141G THR* 6.3 0.7 - - + -
187G ILE* 3.9 29.8 - - + -
189G ILE* 4.0 23.8 - - + -
197G PHE* 4.6 4.3 - - + -
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Residues in contact with PHE 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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13G ALA* 4.2 13.0 - - + +
66G SER* 3.5 2.9 - - - -
67G PHE* 3.0 62.1 + + + +
69G GLU* 4.0 16.8 - - + -
129G SER* 3.8 23.6 - - - -
130G LEU* 1.3 74.5 - - - +
132G ALA* 1.3 66.7 + - - +
135G ILE* 4.4 6.7 - - - -
138G HIS* 3.2 44.4 - + + -
473H LYS* 3.8 24.0 - - + -
475H ILE* 3.6 32.3 - - + -
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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