Contacts of the helix formed by residues 29 - 41 (chain K) in PDB entry 3J7Y
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 GLY 29 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2239A A 3.1 28.5 + - - -
2240A C 4.1 1.5 - - - +
28K PRO* 1.3 71.4 - - - +
30K LYS* 1.3 56.2 + - - -
31K LEU* 3.3 0.6 - - - +
32K ALA* 3.4 29.7 - - - +
33K ALA* 3.0 23.4 + - - +
104K VAL* 5.7 0.4 - - - +
107K ALA* 4.0 7.3 - - - +
111K MET* 3.3 5.7 - - - +
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Residues in contact with LYS 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2240A C 3.6 32.0 - - - +
2241A A 3.6 5.3 + - - -
2242A U 2.4 37.7 + - - -
27K PRO* 3.4 31.2 - - + +
28K PRO 3.1 6.3 + - - -
29K GLY* 1.3 72.7 - - - +
31K LEU* 1.3 64.2 + - - +
33K ALA* 4.0 6.4 + - + +
34K MET* 3.7 10.6 + - - +
148K PRO* 3.6 38.1 + - + +
149K ARG* 5.4 2.8 - - + +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 3.6 42.8 - - + +
22K ASP 4.1 1.6 - - - +
23K GLY* 4.2 18.6 - - - -
26K GLN* 3.7 31.4 - - + +
27K PRO 3.1 16.8 + - - +
28K PRO* 4.6 7.2 - - + -
29K GLY 4.5 2.7 - - - +
30K LYS* 1.3 77.0 - - - +
32K ALA* 1.3 59.0 - - - +
34K MET* 3.0 10.2 + - + +
35K ALA* 2.9 27.8 + - - +
59K ILE* 4.3 17.7 - - + -
62K THR* 5.7 0.4 - - + -
65K ILE* 5.1 6.7 - - + -
104K VAL* 4.7 19.5 - - + -
148K PRO* 4.9 2.7 - - - -
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Residues in contact with ALA 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K GLY* 3.4 24.6 - - - +
31K LEU* 1.3 77.9 - - - +
33K ALA* 1.3 57.2 + - - +
35K ALA* 4.0 1.3 - - - -
36K SER* 2.7 37.2 + - - -
104K VAL* 4.5 1.6 - - + +
107K ALA* 3.8 6.7 - - + -
108K ILE* 3.4 44.1 - - + +
111K MET* 3.9 6.7 - - + -
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Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K GLY 3.0 18.8 + - - +
30K LYS* 4.1 8.1 - - - +
31K LEU 3.2 0.4 + - - -
32K ALA* 1.3 73.2 - - - +
34K MET* 1.3 63.6 + - + +
36K SER* 2.6 19.0 + - - -
37K ILE* 3.0 22.5 + - + +
111K MET* 3.7 16.6 - - + -
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Residues in contact with MET 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 3.5 33.9 - - + -
30K LYS 3.7 13.7 - - - +
31K LEU* 3.0 5.7 + - - +
33K ALA* 1.3 79.0 - - + +
35K ALA* 1.3 57.0 + - - +
37K ILE* 3.2 12.4 + - + +
38K ARG* 2.9 45.8 + - - +
145K LEU* 3.6 18.6 - - + -
146K PRO* 3.7 8.1 - - - +
148K PRO* 3.5 31.9 - - + -
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Residues in contact with ALA 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K LEU* 4.2 4.7 - - + +
31K LEU 2.9 14.6 + - - +
32K ALA 3.8 1.6 - - - +
34K MET* 1.3 77.2 - - - +
36K SER* 1.3 57.6 + - - +
38K ARG* 3.2 4.7 + - - +
39K LEU* 2.8 35.9 + - + +
57K VAL* 3.7 19.8 - - + +
59K ILE* 4.0 15.0 - - + -
108K ILE* 3.8 28.3 - - + -
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Residues in contact with SER 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ALA 2.7 19.1 + - - -
33K ALA* 2.6 22.7 + - - -
35K ALA* 1.3 72.7 - - - +
37K ILE* 1.3 61.4 + - - +
39K LEU* 3.2 7.8 + - - +
40K GLN* 2.9 34.3 + - - +
108K ILE* 4.4 4.4 - - - +
111K MET* 3.3 30.9 + - - +
112K LEU* 3.5 23.4 - - - +
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Residues in contact with ILE 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ALA* 3.0 25.5 + - + +
34K MET* 3.4 10.8 - - + +
36K SER* 1.3 83.6 + - - +
38K ARG* 1.3 66.2 + - - +
40K GLN* 3.2 9.9 + - - +
41K GLY 2.9 24.1 + - - -
42K LEU* 3.2 30.0 + - + -
43K HIS* 3.8 28.2 + - + +
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Residues in contact with ARG 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 3.7 44.7 - - + -
34K MET* 2.9 33.4 + - - +
35K ALA* 3.5 8.7 - - - +
37K ILE* 1.3 91.0 - - - +
39K LEU* 1.3 61.7 + - - +
41K GLY 3.1 9.2 + - - -
43K HIS* 3.5 39.8 - - + +
55K ASP* 3.2 21.0 + - + -
57K VAL* 3.5 15.9 - - + -
145K LEU* 3.6 30.1 - - - +
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Residues in contact with LEU 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ALA* 2.8 17.0 + - + +
36K SER* 3.2 8.0 + - - +
38K ARG* 1.3 75.3 - - - +
40K GLN* 1.3 65.3 + - - +
54K GLY* 3.1 17.3 - - - -
55K ASP 3.8 17.8 - - - +
57K VAL* 4.1 11.4 - - + -
108K ILE* 3.5 31.9 - - + -
112K LEU* 3.8 20.6 - - + -
121K MET* 3.1 43.7 - - + +
122K MET* 4.7 0.7 - - - -
124K ARG* 4.0 6.0 - - + -
125K LEU* 4.0 25.8 - - + +
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Residues in contact with GLN 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K SER* 2.9 28.3 + - - +
37K ILE* 3.2 8.5 + - - +
39K LEU* 1.3 77.8 - - - +
41K GLY* 1.3 59.9 + - - +
42K LEU* 3.1 38.2 - - + +
47K TYR* 4.3 19.3 + - + +
48K HIS 5.5 0.2 - - - +
53K CYS* 4.0 8.0 + - - -
54K GLY* 3.9 8.7 + - - -
111K MET 4.7 5.1 + - - -
112K LEU* 3.9 5.8 - - + +
113K PRO* 3.7 38.3 - - + +
121K MET* 3.6 12.2 - - - +
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Residues in contact with GLY 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ILE 2.9 4.8 + - - -
38K ARG 3.1 13.2 + - - -
40K GLN* 1.3 78.9 - - - +
42K LEU* 1.3 57.3 + - - +
43K HIS* 3.2 12.3 - - - -
44K LYS* 3.1 22.7 + - - +
47K TYR* 3.5 14.7 - - - +
53K CYS* 3.8 25.5 - - - -
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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