Contacts of the strand formed by residues 104 - 109 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51K LEU* 3.7 31.9 - - + -
52K LEU* 3.3 21.6 - - - +
53K GLY 2.9 32.6 + - - -
54K GLN 4.1 0.8 - - - +
55K VAL* 4.1 10.3 - - + +
68K LEU* 3.8 29.5 - - + +
70K VAL* 6.1 2.9 - - + -
95K THR* 3.6 25.4 - - + +
96K ALA* 3.2 28.3 - - - +
97K THR* 3.6 17.2 - - + +
103K GLU* 1.3 74.2 - - - +
105K THR* 1.3 72.7 + - - +
106K LEU* 4.3 10.5 - - + -
128K ILE* 5.0 6.3 - - + -
143K LEU* 4.7 5.4 - - + -
185K PHE* 3.5 39.9 + + + -
187K ILE* 5.2 2.3 - - + +
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Residues in contact with THR 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ASN* 2.8 28.5 + - - +
50K LEU* 4.3 14.1 - - + -
51K LEU 3.2 9.4 - - - -
52K LEU* 4.2 11.9 - - + -
95K THR* 2.8 20.3 + - - -
103K GLU* 4.3 13.0 - - + +
104K TRP* 1.3 83.2 - - - +
106K LEU* 1.3 56.5 - - - +
107K HIS* 4.2 7.0 + - - -
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ASN* 3.4 24.0 - - + +
39K LEU* 4.0 12.6 - - + -
50K LEU* 3.4 7.1 - - - +
51K LEU* 2.8 62.5 + - + +
70K VAL* 3.8 39.5 - - + -
72K GLN* 5.1 3.1 - - - +
94K ARG 4.6 4.0 - - - +
95K THR* 3.8 25.8 - - + -
104K TRP* 4.3 7.6 - - + -
105K THR* 1.3 70.2 - - - +
107K HIS* 1.3 65.2 + - - +
108K THR* 3.9 5.7 + - + -
126K ILE* 5.2 1.8 - - + -
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Residues in contact with HIS 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ASN* 2.9 28.2 + - - +
38K ARG* 3.8 48.1 + - + +
39K LEU* 2.8 29.3 + - - +
40K ALA 3.5 8.5 + - - +
49K ILE 4.1 4.0 - - - -
50K LEU* 3.7 27.2 - - + +
105K THR* 4.2 12.9 + - - -
106K LEU* 1.3 72.8 - - - +
108K THR* 1.3 62.8 + - - +
180K LYS* 5.3 10.3 + - - +
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Residues in contact with THR 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K LEU* 3.9 11.0 - - - +
40K ALA* 4.3 12.6 - - - +
48K HIS* 3.5 10.6 + - - +
49K ILE* 2.9 41.4 + - + +
51K LEU* 3.4 33.4 - - + -
72K GLN* 2.7 29.3 + - - +
89K PHE* 3.8 8.7 - - - -
106K LEU* 4.8 3.4 - - + -
107K HIS* 1.3 77.9 - - - +
109K VAL* 1.3 72.1 + - - +
126K ILE* 4.5 0.7 - - + -
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Residues in contact with VAL 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K ALA* 3.9 18.6 - - + -
44K ALA* 4.7 2.5 - - + -
45K PRO 3.8 19.5 - - - +
46K GLY* 4.5 0.4 - - - -
47K GLU 3.1 16.2 - - - +
48K HIS* 4.2 15.9 - - + +
49K ILE* 4.0 3.4 - - - -
72K GLN* 3.1 20.5 + - - +
74K ASP* 4.3 1.8 - - - -
75K ALA* 3.8 20.4 - - - +
89K PHE* 3.9 22.4 - - + -
108K THR* 1.3 87.1 + - - +
110K LYS* 1.3 78.2 + - - +
111K PRO* 3.5 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