Contacts of the helix formed by residues 15 - 32 (chain K) in PDB entry 2ZJQ
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 SER 15 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K ASN* 2.8 12.4 + - - +
14K SER* 1.3 83.5 + - - +
16K ALA* 1.3 62.8 + - - +
18K VAL* 3.7 11.6 - - - +
19K ALA* 3.5 15.9 + - - +
1288X A 4.7 8.8 + - - -
2669X C 6.0 4.3 - - - -
2689X C 3.5 31.4 + - - -
2690X A 6.0 1.1 - - - -
2692X A 5.8 1.4 + - - -
2693X U 5.1 4.5 - - - -
2694X G 5.8 4.0 - - - -
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Residues in contact with ALA 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ARG* 3.5 33.2 - - + +
13K ASN* 2.5 26.9 - - - +
15K SER* 1.3 70.7 - - - +
17K ARG* 1.3 54.4 - - - +
18K VAL 2.2 19.4 + - - -
19K ALA* 2.4 21.7 + - + +
20K LEU* 2.9 10.6 + - - +
1288X A 4.8 19.7 - - + +
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Residues in contact with ARG 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LYS* 3.3 38.9 + - - +
10K LEU* 2.9 34.9 + - + +
11K ASN* 2.3 42.1 + - - +
12K ARG* 4.2 10.2 - - + +
13K ASN* 4.1 1.5 + - - +
14K SER 3.4 6.0 + - - +
16K ALA* 1.3 76.4 - - - +
18K VAL* 1.3 59.2 + - - +
20K LEU* 2.9 35.5 - - - +
21K ALA* 4.0 14.4 - - - +
39K THR* 4.9 10.3 - - - +
40K LYS* 4.6 13.1 - - - +
43K GLU* 4.2 27.6 + - + +
1668X G 5.1 2.8 + - - -
1669X A 5.1 1.6 + - - -
2669X C 5.9 0.2 - - - +
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Residues in contact with VAL 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K SER 3.5 12.5 + - - +
15K SER* 3.7 15.7 - - - +
16K ALA 2.2 18.2 + - - -
17K ARG* 1.3 71.6 - - - +
19K ALA* 1.3 64.7 + - - +
20K LEU 3.3 0.9 - - - -
21K ALA* 4.1 3.2 + - - +
22K ARG* 3.1 53.2 + - - +
47K PHE* 5.8 0.2 - - - -
2669X C 5.1 20.9 - - + +
2688X G 4.3 9.2 - - - +
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Residues in contact with ALA 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K SER 3.5 6.0 + - - +
16K ALA* 2.4 22.1 + - - +
18K VAL* 1.3 70.7 - - - +
20K LEU* 1.3 71.3 + - - +
22K ARG* 3.0 8.0 + - - +
23K ALA* 2.6 22.0 + - + +
1288X A 3.8 32.3 - - + +
1308X C 3.9 13.7 - - - +
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Residues in contact with LEU 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K ARG* 4.3 15.9 - - - +
16K ALA 2.9 11.6 + - - +
17K ARG* 2.9 41.5 - - - +
19K ALA* 1.3 73.8 - - - +
21K ALA* 1.3 54.6 + - - +
22K ARG 2.3 2.4 + - - -
23K ALA* 2.3 37.4 + - + -
24K GLN* 3.0 32.4 + - + +
40K LYS* 4.2 14.4 - - + -
43K GLU* 4.3 3.6 - - - +
1289X A 4.3 8.5 - - - +
1290X A 3.7 38.6 - - - +
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Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K ARG 4.0 14.5 + - - +
18K VAL* 4.1 4.4 + - - +
19K ALA 3.6 0.4 - - - -
20K LEU* 1.3 78.6 - - - +
22K ARG* 1.3 56.9 + - - +
24K GLN* 4.5 6.3 - - - +
25K ALA* 2.8 27.9 + - - +
43K GLU* 3.4 31.1 + - - +
44K LEU* 3.9 2.6 - - - +
47K PHE* 3.4 27.8 - - + -
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Residues in contact with ARG 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K VAL* 3.1 34.5 + - - +
19K ALA* 3.0 9.1 + - - +
20K LEU 2.3 13.1 + - - -
21K ALA* 1.3 70.2 - - - +
23K ALA* 1.3 59.0 + - - +
25K ALA* 3.3 5.8 - - - +
26K THR* 2.9 34.0 + - - -
47K PHE* 4.3 15.9 - - + -
68K GLN* 3.9 3.9 + - - +
69K ASP* 3.3 34.9 + - + +
71K HIS* 3.5 27.7 + - - +
2687X G 2.8 34.8 + - - -
2688X G 3.2 19.3 + - - -
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Residues in contact with ALA 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K ALA* 2.6 14.3 + - + +
20K LEU* 2.3 29.9 + - - +
22K ARG* 1.3 69.4 - - - +
24K GLN* 1.3 59.5 + - + +
26K THR* 3.9 3.7 + - - -
27K ALA* 3.8 14.6 + - - +
1289X A 5.9 3.8 - - + +
1290X A 4.0 28.6 + - - +
1291X G 5.3 0.2 - - - +
1307X U 5.8 3.4 - - - +
1308X C 5.8 5.2 - - - +
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Residues in contact with GLN 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.0 40.7 + - + +
21K ALA 4.5 1.2 - - - +
23K ALA* 1.3 74.9 - - - +
25K ALA* 1.3 71.1 + - - +
26K THR 3.2 0.4 + - - -
27K ALA* 3.3 4.9 + - - +
28K LEU* 3.1 22.0 + - - +
34K ILE* 4.4 9.9 - - + +
36K THR* 3.7 26.0 + - - +
40K LYS* 3.5 27.4 + - - +
43K GLU* 4.3 6.1 + - - -
44K LEU* 3.4 28.8 - - + +
1290X A 3.9 22.7 - - - +
1291X G 4.4 0.2 + - - -
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Residues in contact with ALA 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K ALA 2.8 24.7 + - - +
22K ARG* 3.3 7.6 - - - +
24K GLN* 1.3 78.8 - - - +
26K THR* 1.3 68.3 + - - +
28K LEU* 3.5 2.6 + - - +
29K LEU* 3.3 21.2 + - - +
44K LEU* 4.0 8.9 - - - +
47K PHE* 3.2 24.9 - - + -
48K VAL* 5.0 7.0 - - + -
51K LEU* 4.3 9.6 - - + -
69K ASP 4.8 2.9 - - - +
70K ILE* 5.1 0.2 - - + -
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Residues in contact with THR 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ARG 2.9 15.5 + - - -
23K ALA* 4.2 4.9 - - - -
24K GLN 3.2 0.2 - - - -
25K ALA* 1.3 72.8 - - - +
27K ALA* 1.3 56.2 + - - +
29K LEU* 2.5 34.3 + - - +
30K ARG* 2.8 27.7 + - - +
69K ASP 4.7 0.2 + - - -
70K ILE* 4.3 25.1 - - - +
71K HIS 5.0 1.7 + - - -
72K ASP* 5.0 5.2 + - + +
75K VAL* 3.5 35.4 - - + -
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ALA 3.8 10.0 + - - +
24K GLN* 3.3 7.7 + - - +
26K THR* 1.3 76.4 - - - +
28K LEU* 1.3 65.9 + - - +
30K ARG* 2.7 17.4 + - - +
31K GLU* 2.6 30.7 + - + +
34K ILE* 4.0 7.9 - - + -
1291X G 3.7 38.4 - - - +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN 3.1 13.8 + - - +
25K ALA 3.9 2.9 - - - +
26K THR 3.0 1.2 + - - -
27K ALA* 1.3 75.6 - - - +
29K LEU* 1.3 59.4 + - + +
32K GLY* 2.6 33.6 + - - +
33K ARG 4.9 0.7 - - - +
34K ILE* 4.1 15.5 - - + +
44K LEU* 4.2 6.5 - - + -
48K VAL* 4.1 16.8 - - + -
95K THR* 4.1 9.4 - - - +
113K ILE* 3.8 48.7 - - + +
115K LEU* 3.1 42.5 - - + +
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Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ALA 3.4 11.4 - - - +
26K THR 2.5 14.3 + - - +
28K LEU* 1.3 76.2 - - + +
30K ARG* 1.3 55.1 + - - -
48K VAL* 3.4 30.5 - - + -
51K LEU* 5.0 7.4 - - + -
52K ILE* 4.5 7.9 - - + -
70K ILE* 3.8 26.0 - - + -
75K VAL* 4.0 11.0 - - + -
78K LYS* 2.9 32.5 + - + +
79K VAL* 3.8 32.8 - - + -
83K VAL* 5.3 7.4 - - + +
115K LEU* 4.2 22.2 - - + +
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Residues in contact with ARG 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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26K THR* 2.8 23.3 + - - +
27K ALA* 2.7 22.4 + - - +
29K LEU* 1.3 73.3 - - - +
31K GLU* 1.3 71.9 + - + +
72K ASP* 3.0 28.5 + - - +
75K VAL* 3.7 21.8 - - + +
78K LYS* 3.4 19.4 + - + +
1290X A 6.2 1.0 - - - -
1291X G 5.9 3.4 + - - +
1306X U 4.2 29.4 + - - -
1307X U 5.4 4.9 + - - -
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Residues in contact with GLU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K ALA* 2.6 26.0 + - - +
30K ARG* 1.3 94.6 + - + +
32K GLY* 1.3 55.3 + - - +
33K ARG* 2.9 26.1 + - - +
34K ILE* 4.0 7.0 - - + -
78K LYS* 4.7 3.6 - - - -
1291X G 3.4 7.4 + - - +
1292X A 2.8 44.9 + - - +
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Residues in contact with GLY 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K LEU* 2.6 25.2 + - - -
29K LEU 4.4 1.0 + - - -
30K ARG 3.9 0.2 - - - -
31K GLU* 1.3 70.0 - - - +
33K ARG* 1.3 57.9 + - - +
78K LYS* 4.7 1.5 - - - +
114K GLU* 3.2 2.9 - - - +
115K LEU* 2.6 52.1 + - - +
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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