Contacts of the strand formed by residues 56 - 62 (chain O) 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 ASP 56 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3117B G 4.7 2.3 + - - -
3118B C 3.2 33.3 - - - +
48O VAL* 4.0 1.3 - - - -
49O THR* 2.8 46.3 + - + +
50O LEU 4.1 1.4 - - - +
51O GLY* 3.8 18.2 - - - -
52O PRO* 4.7 4.6 - - - +
54O GLY 4.3 3.9 - - - +
55O ASP* 1.3 75.2 - - - +
57O THR* 1.3 61.1 + - - +
58O LEU* 2.8 23.0 - - + +
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Residues in contact with THR 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3005B G 3.2 22.3 + - - -
3006B C 5.1 0.5 + - - -
3118B C 2.9 10.6 + - - +
3119B C 3.1 57.1 - - - +
46O GLN* 3.9 14.0 + - + -
47O LEU 3.8 5.2 - - - +
48O VAL* 3.8 15.3 - - - +
55O ASP 4.2 0.4 - - - -
56O ASP* 1.3 70.7 - - - +
58O LEU* 1.3 62.3 + - - +
59O ALA 3.7 23.6 - - - +
60O SER* 4.0 6.3 - - - -
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Residues in contact with LEU 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3119B C 6.0 0.2 - - - -
32O PRO* 6.0 3.8 - - + -
47O LEU 3.1 10.3 + - - +
49O THR* 3.4 29.6 - - + +
56O ASP* 2.8 29.6 - - + +
57O THR* 1.3 73.7 - - - +
59O ALA* 1.3 62.3 + - + +
95O ALA* 3.8 17.9 - - + +
97O VAL* 4.2 27.4 - - + -
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Residues in contact with ALA 59 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3119B C 5.5 0.2 - - - -
46O GLN* 3.4 0.5 - - - -
47O LEU* 2.8 38.6 + - + +
57O THR* 3.5 5.4 - - - +
58O LEU* 1.3 83.1 - - + +
60O SER* 1.3 61.6 + - - +
88O ALA* 4.2 5.0 - - - +
91O ARG* 4.1 7.9 - - + +
92O ALA* 3.5 41.5 - - + +
95O ALA* 4.7 1.8 - - + -
97O VAL* 5.6 0.4 - - + -
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Residues in contact with SER 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3119B C 3.4 21.7 + - - -
3120B A 3.6 20.8 + - - -
44O ARG* 5.5 3.5 - - - -
45O ALA 3.2 11.2 - - - -
46O GLN* 3.8 18.8 - - - -
57O THR* 4.0 0.9 - - - -
59O ALA* 1.3 77.1 - - - +
61O ALA* 1.3 63.2 + - - +
88O ALA* 3.7 3.3 - - - +
91O ARG* 3.1 30.4 + - - +
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Residues in contact with ALA 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O ARG* 3.5 4.2 - - - +
45O ALA 2.8 33.7 + - - -
60O SER* 1.3 76.0 - - - +
62O HIS* 1.3 59.3 + - - +
84O THR* 3.1 34.7 - - + +
87O LEU* 3.9 16.2 - - + -
88O ALA* 3.1 22.0 - - + +
91O ARG* 3.7 6.3 - - - +
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Residues in contact with HIS 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3026B C 4.7 8.3 + - - -
3027B C 4.8 1.6 + - - -
3120B A 5.0 10.1 - - - +
42O HIS* 3.2 45.4 - + + +
43O VAL 3.8 2.5 - - - -
44O ARG* 3.6 48.3 + - + +
61O ALA* 1.3 76.2 - - - +
63O SER* 1.3 65.2 + - - +
64O SER* 2.8 38.0 + - - +
65O ASP* 2.5 37.4 + - - +
66O LEU* 3.8 4.9 + - - +
84O THR* 3.7 4.6 + - - +
87O LEU* 4.8 2.6 - - - +
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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