Contacts of the strand formed by residues 70 - 77 (chain R) in PDB entry 1KD1
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 70 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2403A C 3.3 38.1 + - - +
2404A G 3.4 1.6 + - - -
66R LYS* 3.0 6.5 - - - +
67R GLN 2.6 36.9 + - - +
68R GLY 3.2 0.4 - - - -
69R ASP* 1.3 79.8 - - - +
71R TYR* 1.3 56.4 + - - +
85R ILE* 3.9 10.8 - - + -
86R VAL 4.5 2.2 - - - -
87R THR* 4.1 21.2 - - + +
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Residues in contact with TYR 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R GLU 3.4 8.4 + - - -
32R GLU* 2.8 17.8 + - - +
33R PHE* 2.4 70.4 + + + -
35R ASP* 5.9 0.2 - - - -
63R VAL* 3.7 21.3 - - + -
65R GLY 4.6 0.7 - - - -
66R LYS* 3.6 40.8 + - + -
69R ASP 3.9 9.4 - - - -
70R ALA* 1.3 74.9 - - - +
72R LYS* 1.3 61.1 + - - +
73R VAL* 3.9 6.7 - - + -
84R ILE 3.3 1.2 - - - +
85R ILE* 3.3 4.7 - - - -
86R VAL* 2.7 48.3 + - - +
88R ALA* 4.3 13.9 - - + -
91R LEU* 4.4 10.1 - - + -
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Residues in contact with LYS 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2386A U 4.6 8.0 + - - +
2387A U 6.1 0.7 - - - -
64R GLU* 3.0 44.6 + - - +
65R GLY* 3.0 15.5 + - - +
66R LYS 3.7 19.9 + - - +
67R GLN* 3.9 25.9 + - + +
71R TYR* 1.3 72.7 - - - +
73R VAL* 1.3 62.9 + - - +
74R ASP* 4.9 0.4 - - - +
83R THR* 4.0 16.6 - - + -
84R ILE 3.4 4.9 - - - -
85R ILE* 3.6 22.2 - - + -
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Residues in contact with VAL 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R VAL* 3.8 21.8 - - + -
41R LEU* 4.3 5.8 - - + -
61R GLY* 3.7 12.3 - - - +
62R THR 3.5 27.6 - - - +
63R VAL* 4.6 4.9 - - + -
71R TYR* 4.5 6.1 - - + -
72R LYS* 1.3 75.2 - - - +
74R ASP* 1.3 68.9 + - - +
75R ILE* 3.9 5.8 + - + -
83R THR* 3.3 1.7 - - - -
84R ILE* 2.5 44.5 + - + +
86R VAL* 3.5 29.4 - - + -
91R LEU* 4.2 7.9 - - + -
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Residues in contact with ASP 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R GLY* 3.1 6.4 - - - -
62R THR* 2.9 36.7 + - - +
64R GLU* 3.1 31.8 - - + +
72R LYS 4.9 0.5 - - - +
73R VAL* 1.3 77.2 - - - +
75R ILE* 1.3 62.1 + - - +
81R GLU* 6.0 4.9 - - + -
82R LYS 3.4 4.6 - - - +
83R THR* 3.0 27.0 + - - +
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R LEU* 4.5 3.8 - - + -
56R PHE* 3.7 26.7 - - + -
59R GLN* 3.8 32.8 - - + +
60R THR 5.5 0.9 - - - -
61R GLY* 3.9 17.0 - - - +
73R VAL* 3.9 7.6 + - + -
74R ASP* 1.3 80.7 - - - +
76R VAL* 1.3 69.1 + - - +
77R ASP* 4.5 6.7 - - + +
81R GLU* 3.7 3.1 - - - +
82R LYS* 2.8 43.7 + - + +
84R ILE* 3.2 40.6 - - + -
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Residues in contact with VAL 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018A A 4.8 1.9 - - - +
1019A C 4.5 19.9 + - - +
59R GLN* 4.0 15.8 + - - +
75R ILE* 1.3 83.6 - - - +
77R ASP* 1.3 58.4 + - - +
78R GLY 3.4 25.5 + - - +
79R GLY* 4.2 4.9 - - - -
80R LYS 3.1 16.8 - - - +
81R GLU* 4.2 17.3 - - + -
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Residues in contact with ASP 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2304A G 5.6 0.5 + - - -
2392A C 2.5 33.0 + - - +
2393A C 3.4 14.8 - - - +
56R PHE* 3.5 19.0 - - + -
59R GLN* 4.9 6.8 + - - +
75R ILE* 4.1 5.3 - - + +
76R VAL* 1.3 67.7 - - - +
78R GLY* 1.3 63.0 + - - +
79R GLY 2.8 10.2 + - - -
80R LYS 2.6 18.6 + - - +
82R LYS* 2.6 42.7 + - + +
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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