Contacts of the strand formed by residues 63 - 72 (chain C) in PDB entry 1K4R
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 ALA 63 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C CYS* 4.2 3.6 - - - -
62C HIS* 1.3 83.8 + - - +
64C LYS* 1.3 58.3 + - - +
65C LEU* 4.2 18.4 - - + -
119C ALA* 5.5 2.7 - - + -
120C ALA 3.4 11.9 - - - +
122C GLU* 4.3 2.5 - - - +
226C PRO* 5.8 2.0 - - + -
238C ALA* 5.6 2.2 - - + +
241C LEU* 3.7 31.9 - - + +
242C VAL* 5.0 2.2 - - + -
256C ASN* 2.8 31.5 + - - +
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C HIS 3.7 0.8 + - - -
63C ALA* 1.3 70.5 - - - +
65C LEU* 1.3 65.5 + - - +
66C SER* 4.2 6.5 + - - -
118C LYS 3.7 1.7 - - - +
119C ALA* 3.8 0.3 - - - -
120C ALA* 2.9 42.6 + - + +
121C CYS 4.1 9.0 - - - +
122C GLU* 3.7 40.0 + - - +
123C ALA 5.9 0.2 - - - +
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B HIS* 4.0 29.9 + - + +
63C ALA* 3.8 8.4 + - + -
64C LYS* 1.3 80.0 - - - +
66C SER* 1.3 64.4 + - - +
117C VAL* 4.4 12.3 - - + -
118C LYS 3.3 11.4 - - - +
119C ALA* 3.9 17.0 - - + -
242C VAL* 3.7 32.8 - - + -
254C VAL* 4.1 22.2 - - + -
255C TYR 4.4 0.2 - - - +
256C ASN* 4.0 36.2 - - + +
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B HIS* 5.2 3.6 - - - -
64C LYS* 5.4 6.4 + - - -
65C LEU* 1.3 78.6 - - - +
67C ASP* 1.3 77.3 + - - +
68C THR* 3.5 4.6 + - - -
117C VAL* 3.8 2.3 - - - +
118C LYS* 2.9 46.1 + - - +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER* 1.3 83.2 + - - +
68C THR* 1.3 66.4 + - - +
69C LYS* 3.4 24.4 + - - +
84C GLU* 5.8 2.1 - - - +
116C CYS 3.8 4.7 - - - +
117C VAL* 4.4 1.4 - - - -
118C LYS* 3.0 39.0 + - + +
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLU* 5.3 1.7 + - - -
208B HIS* 3.5 19.0 - - + -
66C SER 3.5 1.1 - - - -
67C ASP* 1.3 74.6 + - - +
69C LYS* 1.3 67.5 + - - +
70C VAL* 4.9 9.4 - - + -
115C ALA* 5.5 0.4 - - + -
116C CYS 3.4 8.3 - - - +
117C VAL* 3.3 16.9 - - + +
252C MET 5.0 3.4 - - - +
254C VAL* 3.7 30.3 - - + +
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ASP* 3.5 21.8 - - - +
68C THR* 1.3 79.4 - - - +
70C VAL* 1.3 64.4 + - - +
82C LEU* 3.4 23.4 - - + +
84C GLU* 2.8 35.8 + - + +
115C ALA* 3.2 4.2 - - - +
116C CYS* 2.8 36.1 + - + +
118C LYS* 6.3 1.1 - - - -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 4.9 6.7 - - + -
69C LYS* 1.3 81.2 - - - +
71C ALA* 1.3 65.8 + - - +
72C ALA* 4.9 0.7 - - + +
82C LEU* 4.4 4.8 - - - +
113C ILE* 3.9 22.4 - - + -
114C VAL 3.3 10.1 - - - +
115C ALA* 3.9 15.3 - - + -
250C VAL 3.5 24.9 - - - +
251C LYS* 4.5 2.7 - - + -
252C MET 4.3 17.5 - - - +
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C VAL* 1.3 75.5 - - - +
72C ALA* 1.3 61.2 + - - +
80C ALA* 3.3 9.4 - - + +
81C THR 3.7 24.2 - - - +
82C LEU* 3.8 15.9 - - + +
113C ILE* 3.3 3.1 - - - +
114C VAL* 2.9 38.2 + - + +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C VAL* 5.1 0.2 - - + -
71C ALA* 1.3 76.0 - - - +
73C ARG* 1.3 69.0 + - - +
80C ALA* 4.0 0.2 - - - -
97C SER* 5.3 0.4 - - - +
99C ARG* 3.8 19.2 + - - +
112C SER 3.2 9.0 - - - +
113C ILE* 4.1 14.8 - - + -
249C ALA 4.6 0.9 - - - +
250C VAL* 4.1 26.2 - - + +
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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