Contacts of the strand formed by residues 104 - 109 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.9 24.9 - - + -
52A LEU* 3.1 38.1 - - - +
53A GLY 2.9 39.5 + - - -
54A GLN 4.0 1.6 + - - +
55A VAL* 4.2 10.5 - - + +
68A LEU* 3.9 29.4 - - + +
70A VAL* 6.1 1.1 - - + -
95A THR* 3.5 34.1 - - + +
96A ALA* 3.6 18.2 - - - +
97A THR* 3.8 15.9 - - + -
103A GLU* 1.3 73.5 - - - +
105A THR* 1.3 74.6 + - - +
106A LEU* 4.3 11.7 - - + -
128A ILE* 5.1 4.5 - - + -
143A LEU* 4.4 13.0 - - + -
185A PHE* 3.4 39.4 + + + -
187A ILE* 5.4 2.1 - - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 3.1 26.6 + - - -
50A LEU* 4.4 15.7 - - + -
51A LEU 3.1 7.6 - - - -
52A LEU* 3.9 13.9 - - + -
95A THR* 2.8 22.1 + - - -
103A GLU* 4.9 9.6 - - + +
104A TRP* 1.3 85.3 - - - +
106A LEU* 1.3 61.9 + - - +
107A HIS* 4.5 5.7 + - - -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 3.4 25.1 - - + +
39A LEU* 4.0 17.0 - - + -
50A LEU* 3.5 6.2 - - - +
51A LEU* 2.9 61.0 + - + +
70A VAL* 3.9 35.4 - - + -
72A GLN* 5.5 0.9 - - - +
94A ARG 4.4 4.0 - - - +
95A THR* 4.0 13.5 - - + -
104A TRP* 4.3 11.0 - - + -
105A THR* 1.3 80.0 - - - +
107A HIS* 1.3 66.3 + - - +
108A THR* 4.0 4.3 + - + -
126A ILE* 5.5 0.9 - - + -
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Residues in contact with HIS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 2.8 26.7 + - - +
38A ARG* 3.2 52.2 + - + +
39A LEU* 2.9 26.0 + - - +
40A ALA 3.5 7.3 + - - +
49A ILE 3.9 3.6 - - - -
50A LEU* 3.5 22.9 - - + +
105A THR* 4.5 8.3 + - - -
106A LEU* 1.3 76.7 - - - +
108A THR* 1.3 61.4 + - - +
180A LYS* 3.5 21.7 + - + +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.6 18.8 - - - +
40A ALA* 4.1 11.0 - - - +
48A HIS* 3.5 10.4 + - - +
49A ILE* 3.0 44.0 + - + +
51A LEU* 4.0 22.9 - - + -
72A GLN* 2.8 36.4 + - - +
89A PHE* 3.8 2.3 - - - -
106A LEU* 5.0 3.6 - - + -
107A HIS* 1.3 77.5 - - - +
109A VAL* 1.3 74.1 + - - +
126A ILE* 4.6 0.7 - - + -
180A LYS* 5.0 1.1 + - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 3.7 19.2 - - + +
44A ALA* 4.6 2.2 - - + -
45A PRO 3.9 24.0 - - - +
46A GLY 4.5 0.4 - - - -
47A GLU 3.2 17.5 - - - +
48A HIS* 4.0 15.7 - - + +
49A ILE* 4.1 3.6 - - - -
72A GLN* 2.7 29.2 + - - +
75A ALA* 4.3 15.3 - - + +
89A PHE* 3.7 23.6 - - + -
108A THR* 1.3 85.1 + - - +
110A LYS* 1.3 68.7 + - - +
111A PRO* 3.3 1.4 - - - +
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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