Contacts of the strand formed by residues 63 - 72 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A CYS* 4.2 3.4 - - - -
62A HIS* 1.3 83.6 + - - +
64A LYS* 1.3 58.7 + - - +
65A LEU* 4.2 18.6 - - + -
119A ALA* 5.5 2.5 - - + -
120A ALA 3.4 12.1 - - - +
122A GLU* 4.3 2.6 - - - +
226A PRO* 5.8 1.8 - - + -
238A ALA* 5.6 2.2 - - + +
241A LEU* 3.7 31.5 - - + +
242A VAL* 5.0 2.2 - - + -
256A ASN* 2.8 32.1 + - - +
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Residues in contact with LYS 64 (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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62A HIS 3.7 0.6 + - - -
63A ALA* 1.3 70.7 - - - +
65A LEU* 1.3 66.2 + - - +
66A SER* 5.4 2.5 + - - -
118A LYS 3.7 1.7 - - - +
119A ALA* 3.8 0.2 - - - -
120A ALA* 2.9 43.2 + - + +
121A CYS 4.1 9.4 - - - +
122A GLU* 3.7 41.1 + - - +
123A ALA 5.9 0.2 - - - +
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Residues in contact with LEU 65 (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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63A ALA* 3.8 8.4 + - + -
64A LYS* 1.3 78.6 - - - +
66A SER* 1.3 66.1 + - - +
117A VAL* 4.4 14.4 - - + -
118A LYS 3.3 11.9 - - - +
119A ALA* 3.9 16.6 - - + -
242A VAL* 3.7 33.2 - - + -
254A VAL* 4.1 22.7 - - + +
256A ASN* 4.0 36.8 - - + +
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Residues in contact with SER 66 (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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64A LYS* 4.2 6.6 + - - -
65A LEU* 1.3 77.6 - - - +
67A ASP* 1.3 76.6 + - - +
68A THR* 3.5 6.0 + - - -
117A VAL* 3.8 2.1 - - - +
118A LYS* 2.9 47.5 + - - +
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Residues in contact with ASP 67 (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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66A SER* 1.3 82.7 + - - +
68A THR* 1.3 67.5 + - - +
69A LYS* 3.4 25.6 + - - +
84A GLU* 5.8 2.1 - - - +
116A CYS 3.8 4.2 - - - +
117A VAL* 4.4 1.6 - - - -
118A LYS* 3.0 38.7 + - + +
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Residues in contact with THR 68 (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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66A SER* 3.5 1.8 - - - -
67A ASP* 1.3 74.8 + - - +
69A LYS* 1.3 67.1 + - - +
70A VAL* 4.9 10.1 - - + -
115A ALA* 5.5 0.2 - - + -
116A CYS 3.4 8.7 - - - +
117A VAL* 3.3 16.5 - - + +
252A MET 5.0 2.9 - - - +
254A VAL* 3.7 31.4 - - + +
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Residues in contact with LYS 69 (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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67A ASP* 3.5 22.9 - - - +
68A THR* 1.3 79.6 - - - +
70A VAL* 1.3 63.5 + - - +
82A LEU* 3.4 21.9 - - + +
84A GLU* 2.8 36.1 + - + +
115A ALA* 3.2 4.7 - - - +
116A CYS* 2.8 35.7 + - + +
118A LYS* 6.3 0.9 - - - -
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Residues in contact with VAL 70 (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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68A THR* 4.9 7.0 - - + -
69A LYS* 1.3 81.6 - - - +
71A ALA* 1.3 66.3 + - - +
72A ALA* 5.1 0.2 - - + -
82A LEU* 4.4 5.1 - - - +
113A ILE* 3.9 22.2 - - + -
114A VAL 3.3 10.8 - - - +
115A ALA* 3.9 15.0 - - + -
250A VAL 3.5 25.4 - - - +
251A LYS* 4.5 2.2 - - + -
252A MET 4.3 17.7 - - - +
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Residues in contact with ALA 71 (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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70A VAL* 1.3 75.5 - - - +
72A ALA* 1.3 60.6 + - - +
80A ALA* 3.3 9.5 - - + +
81A THR 3.7 23.6 - - - +
82A LEU* 3.8 16.4 - - + +
113A ILE* 3.3 3.5 - - - +
114A VAL* 2.9 39.0 + - + -
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Residues in contact with ALA 72 (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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70A VAL* 4.9 0.2 - - - +
71A ALA* 1.3 76.9 - - - +
73A ARG* 1.3 69.4 + - - +
80A ALA* 4.0 0.2 - - - -
97A SER* 5.3 0.4 - - - +
99A ARG* 3.8 18.9 + - - +
112A SER 3.2 8.5 - - - +
113A ILE* 4.1 14.6 - - + -
249A ALA 4.6 0.9 - - - +
250A 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