Contacts of the helix formed by residues 38 - 50 (chain H) in PDB entry 3KDO
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 THR 38 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H PRO* 4.4 0.7 - - - -
37H TYR* 1.3 77.0 - - - +
39H ILE* 1.3 64.0 - - - +
40H GLU* 3.5 17.8 + - - +
41H GLN* 2.8 44.2 + - - +
42H ALA* 3.1 19.4 + - - +
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Residues in contact with ILE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 3.6 38.6 - - + +
33H PRO* 4.2 7.8 - - + +
37H TYR 3.9 0.6 + - - -
38H THR* 1.3 72.5 - - - +
40H GLU* 1.3 86.5 + - - +
42H ALA* 2.8 4.6 + - + +
43H ALA* 2.7 33.6 + - - +
77H PHE* 3.8 24.2 - - + -
85H TRP* 3.6 63.9 - - + +
87H VAL* 4.1 4.5 - - + -
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Residues in contact with GLU 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ASP* 4.9 3.5 - - - +
13H VAL* 3.4 21.8 - - + +
15H LYS* 2.8 39.8 + - - +
38H THR* 3.2 19.1 + - - +
39H ILE* 1.3 95.9 - - + +
41H GLN* 1.3 57.1 + - + +
44H GLY* 2.8 27.9 + - - -
77H PHE* 4.3 9.7 - - + -
85H TRP* 5.9 1.0 - - - -
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H TYR* 4.7 0.2 - - - +
10H ASP* 4.4 14.3 + - - +
36H GLY 4.4 2.3 + - - +
37H TYR* 3.5 20.7 - - + -
38H THR* 2.8 51.6 + - - +
39H ILE 3.1 0.2 - - - -
40H GLU* 1.3 76.7 - - + +
42H ALA* 1.3 61.2 + - - +
44H GLY* 3.6 1.2 + - - -
45H ALA 3.2 15.1 + - - -
117H ARG* 3.1 42.8 + - - +
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Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 3.7 22.7 - - + -
33H PRO* 3.9 20.6 - - + -
37H TYR* 5.4 1.3 - - + +
38H THR 3.1 11.1 + - - +
39H ILE* 2.8 8.6 + - - +
41H GLN* 1.3 73.6 - - - +
43H ALA* 1.3 61.0 + - - +
45H ALA* 2.8 25.4 + - - +
46H VAL* 2.9 17.8 + - + +
115H MET* 5.2 0.2 - - - +
117H ARG* 4.7 12.3 - - - +
118H VAL* 5.5 3.8 - - + -
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Residues in contact with ALA 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H VAL* 4.6 4.0 - - - +
39H ILE* 2.7 19.3 + - - +
40H GLU 4.1 0.7 - - - +
42H ALA* 1.3 73.5 - - - +
44H GLY* 1.3 56.8 + - - +
46H VAL* 3.1 9.4 + - - +
47H ALA* 2.9 32.9 + - - +
74H ALA* 4.1 6.5 - - + +
77H PHE* 3.6 29.6 - - + -
87H VAL* 3.8 24.7 - - + -
89H ILE* 4.4 1.4 - - + +
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Residues in contact with GLY 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TYR* 3.3 28.9 - - - +
12H TYR* 3.9 5.6 - - - +
13H VAL* 3.8 10.0 - - - +
40H GLU 2.8 20.5 + - - -
41H GLN 3.9 1.6 - - - -
43H ALA* 1.3 77.6 - - - +
45H ALA* 1.3 57.3 + - - +
48H ALA* 3.1 29.5 + - - +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H TYR* 3.5 22.2 - - + +
41H GLN 3.2 12.9 + - - +
42H ALA* 2.8 10.6 + - - +
44H GLY* 1.3 75.4 - - - +
46H VAL* 1.3 59.2 + - - +
48H ALA* 3.9 0.2 - - - +
49H GLU* 2.9 36.6 + - - +
115H MET* 4.1 18.6 - - + -
117H ARG* 4.1 22.0 - - + +
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 4.3 16.6 - - + -
31H VAL* 4.7 8.3 - - + -
42H ALA 2.9 21.0 + - - +
43H ALA* 3.6 8.5 - - - +
45H ALA* 1.3 75.2 - - - +
47H ALA* 1.3 58.9 + - - +
50H SER* 2.7 35.2 + - - +
89H ILE* 3.8 18.4 - - + -
112H ILE* 3.6 9.9 - - + +
115H MET* 3.9 20.6 - - + -
118H VAL* 5.5 4.0 - - + -
121H LEU* 4.1 34.5 - - + -
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H TYR* 3.9 26.7 - - + +
43H ALA 2.9 19.4 + - - +
46H VAL* 1.3 73.8 - - - +
48H ALA* 1.3 59.4 + - - +
50H SER* 3.3 14.5 + - - -
51H SER* 2.9 21.7 + - - -
72H ALA* 3.9 6.9 - - + +
74H ALA 4.3 3.6 - - - +
89H ILE* 3.7 31.6 - - + +
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Residues in contact with ALA 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ILE* 5.8 0.2 - - + -
9H TYR* 3.4 22.0 - - + -
12H TYR* 3.3 36.5 - - + -
44H GLY 3.1 21.3 + - - +
46H VAL 3.2 0.6 - - - -
47H ALA* 1.3 78.7 - - - +
49H GLU* 1.3 60.5 + - - +
50H SER 3.3 0.7 + - - -
51H SER 3.4 6.1 + - - -
52H THR 3.4 0.2 + - - -
53H GLY* 2.7 31.4 + - - +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LYS* 5.5 0.7 + - - -
165A LYS* 3.3 26.2 + - - +
192A GLU* 4.8 1.7 - - - +
322A LYS* 3.5 25.8 + - - +
600A CAP 4.0 14.6 - - - +
9H TYR* 2.7 30.3 + - + +
45H ALA 2.9 20.9 + - - +
48H ALA* 1.3 75.8 - - - +
50H SER* 1.3 57.3 + - - +
51H SER 3.4 1.6 - - - -
53H GLY 3.7 13.5 - - - +
54H THR* 3.6 7.3 - - - -
107H SER* 4.9 0.5 - - - +
111H ASN* 5.4 10.6 + - + +
112H ILE* 4.0 13.8 + - + +
115H MET* 3.5 24.7 - - + -
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Residues in contact with SER 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN* 4.7 2.0 - - - -
46H VAL* 2.7 22.3 + - - +
47H ALA* 3.3 5.5 + - - -
49H GLU* 1.3 78.4 - - - +
51H SER* 1.3 56.3 + - - +
91H TYR* 2.7 36.7 + - - -
96H PHE* 5.1 0.5 - - - -
107H SER* 3.0 48.9 + - - +
108H ILE* 4.4 2.9 - - - -
112H ILE* 3.9 12.8 - - - -
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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