Contacts of the helix formed by residues 38 - 56 (chain K) in PDB entry 2ZJR
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 LEU 38 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K THR 3.3 1.4 + - - -
37K THR* 1.3 74.6 - - - +
39K THR* 1.3 66.2 + - - +
41K ALA* 3.3 3.1 + - - +
42K LYS* 3.2 41.1 + - + +
97K ILE* 4.2 15.7 - - + -
99K ARG* 4.6 17.9 - - + +
108K VAL* 5.3 0.4 - - - +
109K THR* 3.2 39.5 + - + +
110K MET* 4.3 0.2 - - - +
111K ALA* 3.9 23.8 - - + -
2791X C 6.1 0.9 - - - +
2792X C 4.5 14.4 - - - +
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Residues in contact with THR 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LYS* 3.6 29.8 - - + +
17K ARG* 5.0 5.8 - - - +
37K THR* 3.2 1.6 - - - -
38K LEU* 1.3 79.3 - - - +
40K LYS* 1.3 61.8 + - - +
42K LYS* 2.7 29.5 + - - +
43K GLU* 2.9 10.6 + - - +
1668X G 3.7 50.3 + - - +
1669X A 4.1 2.9 - - - +
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Residues in contact with LYS 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ARG* 3.2 25.3 - - - +
17K ARG* 4.6 8.3 - - - +
20K LEU* 3.7 21.5 - - + -
24K GLN* 3.7 15.2 + - - +
36K THR* 3.9 13.9 - - - +
37K THR* 2.7 31.6 + - - +
39K THR* 1.3 77.8 - - - +
41K ALA* 1.3 57.5 + - - +
43K GLU* 3.1 11.0 + - - +
44K LEU* 2.8 27.0 + - - +
1290X A 2.6 41.3 + - - -
1291X G 5.5 1.0 + - - -
1667X A 4.9 5.5 + - - -
1668X G 3.0 23.3 - - - +
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Residues in contact with ALA 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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24K GLN* 5.1 0.2 - - - -
36K THR* 3.4 22.8 - - + +
37K THR 3.2 3.2 + - - +
38K LEU* 3.5 10.5 - - - +
39K THR 3.1 0.4 - - - -
40K LYS* 1.3 78.0 - - - +
42K LYS* 1.3 59.7 + - - +
44K LEU* 3.0 8.2 + - - +
45K ARG* 2.8 32.6 + - - +
97K ILE* 4.3 16.2 - - + -
111K ALA* 5.2 2.9 - - + -
113K ILE* 3.7 24.0 - - + +
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Residues in contact with LYS 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LYS* 4.1 22.0 - - - +
38K LEU* 3.2 34.7 + - + +
39K THR* 2.7 15.3 + - - +
41K ALA* 1.3 78.7 - - - +
43K GLU* 1.3 61.4 + - - +
45K ARG* 3.7 2.2 + - - +
46K PRO* 3.2 18.9 - - - +
97K ILE* 4.3 15.3 - - + -
2792X C 3.5 35.7 + - - -
2793X G 3.3 37.3 + - - +
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Residues in contact with GLU 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ARG* 5.8 1.6 + - - -
9K LYS* 5.0 19.2 - - + +
17K ARG* 4.8 28.2 - - + +
20K LEU* 4.5 3.8 - - - +
21K ALA* 3.1 43.2 + - - +
24K GLN* 3.7 11.1 + - - -
39K THR 2.9 10.4 + - - +
40K LYS* 3.3 11.7 - - - +
42K LYS* 1.3 79.5 - - - +
44K LEU* 1.3 68.0 + - - +
46K PRO* 3.3 14.5 - - - +
47K PHE* 3.8 10.0 + - - +
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Residues in contact with LEU 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA* 3.8 10.1 - - - +
24K GLN* 3.3 51.1 - - + +
25K ALA* 3.3 18.4 - - + +
28K LEU* 4.0 16.6 - - + -
34K ILE* 4.2 9.9 - - + -
40K LYS 2.8 13.3 + - - +
41K ALA* 3.4 9.0 - - - +
43K GLU* 1.3 85.5 - - - +
45K ARG* 1.3 65.3 + - - +
47K PHE* 3.1 7.3 + - + +
48K VAL* 2.9 26.1 + - + +
113K ILE* 3.9 18.8 - - + -
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Residues in contact with ARG 45 (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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41K ALA 2.8 17.6 + - - +
42K LYS* 4.0 2.8 + - - +
44K LEU* 1.3 70.2 - - - +
46K PRO* 1.3 76.7 - - + +
48K VAL* 2.9 24.3 - - - +
49K GLU* 3.1 20.0 + - - +
95K THR* 3.3 30.1 + - + -
96K ARG* 5.3 0.6 - - - +
97K ILE* 3.3 28.0 - - + +
113K ILE* 3.7 7.8 - - + +
2792X C 5.9 1.0 + - - -
2793X G 5.8 1.8 + - - -
2812X A 4.3 6.7 + - - -
2813X G 4.2 29.2 + - - +
2856X U 3.5 44.8 + - - -
2857X C 4.9 7.7 + - - -
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Residues in contact with PRO 46 (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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42K LYS 3.2 21.5 - - - +
43K GLU* 3.3 11.4 - - - +
45K ARG* 1.3 86.2 - - + +
47K PHE* 1.3 72.0 + - - +
49K GLU* 2.9 13.3 + - + +
50K GLN* 3.0 18.6 + - - +
2813X G 3.5 29.8 - - - +
2814X G 4.0 18.1 - - - +
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Residues in contact with PHE 47 (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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8K ARG* 5.9 6.7 - - - +
21K ALA* 3.1 31.2 - - + -
22K ARG* 4.4 6.7 - - + -
25K ALA* 3.0 32.5 - - + -
43K GLU* 3.8 15.3 - - - +
44K LEU* 3.1 12.2 + - + +
46K PRO* 1.3 85.4 - - - +
48K VAL* 1.3 65.5 + - - +
50K GLN* 2.9 26.1 + - + +
51K LEU* 3.1 29.0 + - + +
69K ASP* 4.1 22.9 - - + -
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Residues in contact with VAL 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ALA* 4.7 7.4 - - - +
28K LEU* 3.7 29.6 - - + -
29K LEU* 3.7 32.8 - - + -
44K LEU* 2.9 24.8 + - + +
45K ARG* 2.9 29.2 - - - +
47K PHE* 1.3 81.6 - - + +
49K GLU* 1.3 65.6 + - + +
51K LEU* 2.9 7.7 + - + +
52K ILE* 2.8 25.2 + - + +
95K THR* 4.0 9.4 - - - +
115K LEU* 5.1 2.2 - - + -
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Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K ARG* 3.1 26.4 + - - +
46K PRO* 2.9 8.1 + - - +
48K VAL* 1.3 77.6 - - + +
50K GLN* 1.3 62.6 + - - +
52K ILE* 2.7 34.7 - - + +
53K THR* 2.9 7.8 + - - -
93K GLY* 4.2 3.7 - - - -
94K TYR 4.1 14.9 + - - +
95K THR* 3.2 42.4 + - + +
2813X G 4.6 3.6 + - - -
2814X G 2.3 58.2 + - - +
2815X C 3.6 2.6 + - - -
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Residues in contact with GLN 50 (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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8K ARG* 5.1 6.5 - - - +
46K PRO* 3.0 14.3 + - - +
47K PHE* 2.9 24.1 + - + +
49K GLU* 1.3 77.5 - - - +
51K LEU* 1.3 64.5 + - - +
53K THR* 2.8 14.9 + - - -
54K THR* 3.0 17.2 + - - +
2814X G 4.4 24.7 + - - +
2815X C 3.8 15.0 + - - +
2846X G 5.3 1.0 - - - +
2847X G 3.1 33.1 + - - -
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Residues in contact with LEU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ALA* 4.3 3.1 - - + -
29K LEU* 4.8 8.3 - - + -
47K PHE* 3.1 29.1 + - + +
48K VAL* 2.9 15.4 + - + +
50K GLN* 1.3 80.0 - - - +
52K ILE* 1.3 62.5 + - - +
54K THR* 3.0 17.1 + - - +
55K ALA* 3.1 12.5 + - - +
66K VAL* 3.6 37.7 - - + +
69K ASP* 3.6 35.7 - - + +
70K ILE* 3.6 17.3 - - + -
79K VAL* 5.2 1.8 - - + -
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Residues in contact with ILE 52 (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 LEU* 4.2 23.1 - - + -
48K VAL* 2.8 25.4 + - + +
49K GLU* 2.7 32.1 - - + +
51K LEU* 1.3 72.1 - - - +
53K THR* 1.3 61.2 + - - +
55K ALA* 3.3 8.3 + - - +
56K LYS* 3.0 31.0 + - + +
79K VAL* 4.6 4.7 - - + -
83K VAL* 4.8 14.1 - - + -
84K ALA* 4.2 4.3 - - - +
87K TYR* 4.7 24.9 - - + -
90K ARG* 6.2 0.7 - - - -
92K GLY* 4.8 14.1 - - - -
94K TYR 4.2 25.4 - - - +
115K LEU* 4.9 8.5 - - + -
2814X G 5.6 0.2 - - - +
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Residues in contact with THR 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLU 2.9 7.1 + - - -
50K GLN* 2.8 7.6 + - - -
52K ILE* 1.3 79.8 - - - +
54K THR* 1.3 64.2 + - - +
56K LYS* 3.6 30.3 + - + +
92K GLY* 4.9 2.4 - - - -
2815X C 2.4 42.1 + - - +
2816X C 4.4 18.4 - - - +
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Residues in contact with THR 54 (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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50K GLN* 3.0 13.2 + - - +
51K LEU* 3.0 12.5 + - + +
53K THR* 1.3 78.4 - - - +
55K ALA* 1.3 63.2 + - - +
56K LYS 3.1 0.7 + - - -
57K GLY 3.8 1.9 + - - -
62K SER* 3.1 47.1 + - - +
65K LEU* 3.7 32.8 - - + -
66K VAL* 3.7 9.4 - - + +
2846X G 4.1 12.9 + - - +
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Residues in contact with ALA 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LEU 3.1 7.2 + - - +
52K ILE 3.5 7.4 - - - +
54K THR* 1.3 80.1 - - - +
56K LYS* 1.3 51.0 + - - +
57K GLY 2.8 13.4 + - - -
58K GLY 3.5 5.4 + - - -
66K VAL* 3.6 10.9 - - + +
79K VAL* 3.2 35.2 - - + -
80K MET* 3.4 34.0 - - + +
84K ALA* 3.7 13.2 - - + +
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Residues in contact with LYS 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K ILE* 3.0 20.9 + - + +
53K THR* 3.6 28.1 + - + +
54K THR 3.1 1.0 - - - -
55K ALA* 1.3 73.7 - - - +
57K GLY* 1.3 54.2 + - - +
84K ALA* 3.7 26.2 - - + +
87K TYR* 3.4 16.8 + - + +
88K ALA* 3.6 19.8 + - - +
90K ARG 3.1 25.5 + - - -
91K PRO* 5.1 0.6 - - - +
92K GLY* 4.0 12.1 - - - +
2815X C 6.0 0.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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