Contacts of the strand formed by residues 104 - 109 (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 TRP 104 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G LEU* 3.9 32.1 - - + -
52G LEU* 3.4 26.7 - - - +
53G GLY 3.1 34.4 + - - -
54G GLN 4.0 2.0 + - - +
55G VAL* 4.0 13.8 - - + +
68G LEU* 3.9 23.5 - - + +
70G VAL* 6.1 1.6 - - + -
95G THR* 3.5 28.7 - - + +
96G ALA* 3.2 25.1 - - - +
97G THR* 3.6 17.8 - - + +
103G GLU* 1.3 75.0 - - - +
105G THR* 1.3 75.2 + - - +
106G LEU* 4.3 13.0 - - + -
128G ILE* 5.2 4.5 - - + -
143G LEU* 4.6 7.4 - - + -
185G PHE* 3.7 35.4 + + + -
187G ILE* 5.3 2.3 - - + +
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Residues in contact with THR 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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37G ASN* 3.1 21.2 + - - -
50G LEU* 4.4 15.3 - - + -
51G LEU 3.3 6.7 - - - -
52G LEU* 3.9 15.5 - - + -
95G THR* 2.9 20.7 + - - -
103G GLU* 4.7 11.9 - - + +
104G TRP* 1.3 84.3 - - - +
106G LEU* 1.4 64.6 + - - +
107G HIS* 4.4 7.0 + - - -
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Residues in contact with LEU 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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37G ASN* 3.6 21.5 - - + +
39G LEU* 3.8 26.0 - - + -
49G ILE 4.0 0.2 - - - +
50G LEU* 3.7 5.9 - - - +
51G LEU* 3.0 59.6 + - + +
70G VAL* 3.9 35.0 - - + -
72G GLN* 5.4 0.7 - - - +
94G ARG 4.5 4.9 - - - +
95G THR* 4.1 16.2 - - + -
104G TRP* 4.3 11.7 - - + -
105G THR* 1.4 74.6 - - - +
107G HIS* 1.3 67.4 + - - +
108G THR* 3.9 5.0 + - + -
126G ILE* 5.3 3.1 - - + -
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Residues in contact with HIS 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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37G ASN* 2.8 24.6 + - - +
38G ARG* 3.5 54.2 + - + +
39G LEU* 2.7 33.3 + - - +
40G ALA* 3.5 6.4 + - - +
49G ILE 3.9 4.9 - - - +
50G LEU* 3.6 26.4 - - + +
105G THR* 4.4 9.5 + - - -
106G LEU* 1.3 77.9 - - - +
108G THR* 1.3 59.1 + - - +
180G LYS* 3.9 18.6 + - - +
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Residues in contact with THR 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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39G LEU* 3.9 12.8 - - - +
40G ALA* 4.0 14.1 - - - +
48G HIS* 3.6 7.3 + - - +
49G ILE* 3.0 35.0 + - + +
51G LEU* 3.5 32.5 - - + -
72G GLN* 2.7 32.8 + - - +
89G PHE* 3.8 7.3 - - - -
106G LEU* 4.6 4.9 - - + +
107G HIS* 1.3 77.9 - - - +
109G VAL* 1.3 74.5 + - - +
126G ILE* 4.6 0.4 - - + -
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Residues in contact with VAL 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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40G ALA* 4.0 10.8 - - + -
44G ALA* 4.7 1.8 - - + +
45G PRO 3.6 25.6 - - - +
46G GLY* 4.6 0.4 - - - -
47G GLU 3.3 17.0 - - - +
48G HIS* 4.0 21.3 - - + +
49G ILE* 4.0 4.6 - - - +
72G GLN* 2.9 26.2 + - - +
74G ASP* 5.3 0.2 - - + -
75G ALA* 4.1 19.5 - - + +
89G PHE* 3.8 25.8 - - + -
108G THR* 1.3 83.7 + - - +
110G LYS* 1.3 64.5 + - - +
111G PRO* 3.3 1.9 - - - +
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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