Contacts of the strand formed by residues 23 - 28 (chain T) 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 LYS 23 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1447A U 5.3 1.4 + - - +
1507A C 3.0 34.1 + - - -
1508A C 3.7 13.9 + - - -
14T ALA 4.6 0.9 - - - +
17T ASP* 3.1 26.9 + - + +
18T MET* 3.0 29.5 + - - +
21T GLN* 2.6 37.1 + - + +
22T ASN* 1.3 77.1 - - - +
24T LEU* 1.3 64.9 + - - +
25T GLN* 5.9 0.2 - - + -
51T GLN* 5.8 2.2 - - - +
53T ASN* 6.3 0.7 - - - +
65T VAL* 3.5 29.2 - - + +
66T VAL 3.1 6.5 - - - +
67T ARG* 3.6 34.3 - - + +
74T ALA* 3.9 2.0 - - - +
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Residues in contact with LEU 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T MET* 4.4 6.1 - - + -
23T LYS* 1.3 76.5 - - - +
25T GLN* 1.3 62.6 + - - +
26T PHE* 3.6 29.7 - - + -
41T VAL* 5.4 3.4 - - + -
45T TYR* 5.5 2.2 - - + -
47T VAL* 6.0 0.7 - - + -
64T ALA 3.6 1.0 - - - +
66T VAL* 2.6 40.6 + - + +
68T LEU* 3.8 26.7 - - + -
74T ALA* 3.9 31.2 - - + +
77T VAL* 4.0 21.8 - - + -
78T ALA* 3.9 18.2 - - + -
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Residues in contact with GLN 25 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1445A G 4.6 1.2 + - - -
1447A U 5.6 1.6 + - - -
8T PRO* 3.6 7.4 - - - +
9T HIS* 2.8 55.8 + - + +
11T THR* 4.6 0.5 + - - -
13T LYS* 4.2 10.0 + - - +
14T ALA* 3.4 31.6 + - + +
17T ASP* 3.6 26.6 + - + +
23T LYS 4.3 0.6 + - - -
24T LEU* 1.3 74.9 - - - +
26T PHE* 1.3 64.7 + - - +
63T LYS* 4.1 14.5 + - + +
64T ALA 3.2 3.1 - - - +
65T VAL* 3.9 30.7 - - + +
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Residues in contact with PHE 26 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ILE* 3.9 20.0 - - + -
7T HIS 3.5 9.0 - - - +
8T PRO* 4.1 13.0 - - + -
9T HIS* 3.9 6.3 - - - +
24T LEU* 3.6 47.1 - - + -
25T GLN* 1.3 78.7 - - - +
27T ALA* 1.3 63.4 - - - +
28T VAL* 3.6 18.0 + - + +
37T VAL* 5.7 0.2 - - + -
41T VAL* 4.1 23.8 - - + -
45T TYR* 3.6 39.0 - + - -
63T LYS* 3.4 7.1 - - - +
64T ALA* 2.9 34.7 + - + +
66T VAL* 4.1 14.1 - - + -
81T ILE* 5.8 0.7 - - + -
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Residues in contact with ALA 27 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ILE* 4.2 0.2 - - - -
6T LYS* 2.7 34.7 + - + +
7T HIS* 2.7 48.2 + - + +
9T HIS* 4.3 9.1 - - + +
26T PHE* 1.3 72.4 - - - +
28T VAL* 1.3 60.3 + - - +
61T GLU* 4.4 9.4 - - + +
62T LYS 3.5 6.7 - - - +
63T LYS* 4.9 0.9 - - - +
8312T NA 4.2 6.3 - - - -
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Residues in contact with VAL 28 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T VAL* 3.4 17.5 - - + +
5T ILE* 4.4 9.0 - - + -
6T LYS* 4.2 12.7 + - - +
26T PHE* 3.9 19.1 - - + +
27T ALA* 1.3 79.0 - - - +
29T ASP* 1.3 67.1 + - - +
30T ASP 3.3 2.9 + - - -
32T ALA* 4.6 0.4 - - + -
37T VAL* 4.2 27.1 - - + -
61T GLU* 4.8 0.3 - - - +
62T LYS* 2.8 58.5 + - + +
64T ALA* 4.1 17.3 - - + -
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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