Contacts of the helix formed by residues 13 - 32 (chain K) in PDB entry 6T9L
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 ASN 13 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLN 4.5 1.0 + - - +
10K VAL 3.4 4.9 + - - +
11K PHE 3.2 5.1 - - - +
12K GLN* 1.3 78.8 - - - +
14K GLU* 1.3 72.4 + - - +
15K LYS* 3.6 10.8 + - - +
16K SER* 3.3 37.0 - - - +
17K LYS* 3.3 25.6 + - - +
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Residues in contact with GLU 14 (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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12K GLN 4.0 1.0 + - - -
13K ASN* 1.3 78.5 + - - +
15K LYS* 1.3 59.5 + - - +
16K SER 3.3 0.2 - - - -
17K LYS* 3.2 11.6 + - - +
18K ASP* 2.8 51.9 + - - +
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Residues in contact with LYS 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13K ASN* 3.6 10.4 + - - +
14K GLU* 1.3 78.4 - - - +
16K SER* 1.3 57.8 + - - +
18K ASP* 4.1 11.8 - - + +
19K GLY* 2.9 34.1 + - - +
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Residues in contact with SER 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K VAL* 2.8 39.9 + - - +
13K ASN* 3.3 27.9 - - - +
14K GLU 3.3 0.2 - - - -
15K LYS* 1.3 80.5 - - - +
17K LYS* 1.3 61.0 + - - +
19K GLY* 3.4 1.7 + - - -
20K VAL* 3.3 28.4 + - - +
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Residues in contact with LYS 17 (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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10K VAL 4.0 8.1 - - - +
11K PHE* 3.6 46.3 + - + +
13K ASN 3.3 15.0 + - - +
14K GLU* 3.2 10.7 + - - +
16K SER* 1.3 79.3 + - - +
18K ASP* 1.3 73.5 + - - +
20K VAL* 3.2 9.3 - - + +
21K LEU* 3.1 36.3 + - + +
108K LEU* 4.0 17.0 - - + +
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Residues in contact with ASP 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K GLU* 2.8 40.6 + - - +
15K LYS* 3.9 15.7 + - + +
17K LYS* 1.3 85.2 - - - +
19K GLY* 1.3 57.3 + - - +
21K LEU* 3.8 9.6 - - - +
22K LYS* 3.0 30.7 + - - +
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Residues in contact with GLY 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K LYS* 2.9 29.7 + - - +
16K SER* 3.4 2.4 + - - -
17K LYS 3.2 0.2 - - - -
18K ASP* 1.3 78.6 - - - +
20K VAL* 1.3 60.7 + - - +
22K LYS* 3.4 6.8 + - - +
23K THR* 3.3 23.2 + - - +
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ILE* 5.7 4.5 - - + -
10K VAL* 5.1 19.1 - - + -
11K PHE* 5.3 4.9 - - + -
16K SER 3.3 14.1 + - - +
17K LYS* 3.2 22.7 - - + +
19K GLY* 1.3 76.9 - - - +
21K LEU* 1.3 68.4 + - + +
23K THR* 3.3 18.1 - - - +
24K CYS* 3.2 15.6 - - - +
61K LEU* 3.7 33.2 - - + +
62K GLN* 6.3 0.7 - - + +
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Residues in contact with LEU 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K PHE* 5.8 2.0 - - + -
17K LYS* 3.1 31.7 + - + +
18K ASP* 4.0 10.5 - - - +
20K VAL* 1.3 81.4 - - + +
22K LYS* 1.3 59.1 + - - +
24K CYS* 3.2 14.2 - - - -
25K ASN* 2.9 25.3 + - - -
108K LEU* 3.9 37.9 - - + +
109K ILE* 4.2 24.0 - - + -
112K ALA* 3.9 21.1 - - + -
115K ALA* 4.3 20.0 - - + -
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Residues in contact with LYS 22 (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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18K ASP 3.0 19.1 + - - +
19K GLY* 3.8 7.4 - - - +
20K VAL 3.3 0.4 - - - -
21K LEU* 1.3 78.0 - - - +
23K THR* 1.3 66.1 + - - +
24K CYS 3.4 0.2 - - - -
25K ASN* 3.7 6.7 + - - +
26K ALA* 3.4 25.4 + - - +
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Residues in contact with THR 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K GLY 3.3 12.7 + - - +
20K VAL* 3.3 14.6 - - + +
22K LYS* 1.3 82.6 - - - +
24K CYS* 1.3 57.9 + - - +
26K ALA* 3.3 6.6 + - - +
27K ALA* 2.7 34.2 + - - +
61K LEU* 3.7 33.2 + - + +
32N TRP* 3.2 28.6 - - - -
33N LYS* 4.9 3.2 - - - -
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Residues in contact with CYS 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K VAL 3.2 13.7 - - - +
21K LEU* 3.2 30.7 - - - -
23K THR* 1.3 79.5 - - + +
25K ASN* 1.3 57.7 + - - +
27K ALA* 3.6 7.6 - - - +
28K ARG* 2.7 51.0 + - + +
61K LEU* 6.0 1.8 - - + -
87K ILE* 5.1 16.6 - - + -
109K ILE* 5.4 5.8 - - - -
112K ALA* 3.9 17.9 - - - -
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Residues in contact with ASN 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K LEU 2.9 19.2 + - - -
22K LYS* 3.7 8.9 + - - +
23K THR 3.3 0.2 - - - -
24K CYS* 1.3 78.7 - - - +
26K ALA* 1.3 57.4 + - - +
28K ARG* 4.1 10.7 + - - +
29K TYR* 3.1 26.3 + - - +
112K ALA* 2.4 47.8 + - - +
113K ILE* 3.2 26.3 + - + +
115K ALA* 4.8 1.6 - - - +
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Residues in contact with ALA 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K LYS* 3.4 19.6 + - - +
23K THR* 3.3 10.6 + - - +
24K CYS 3.2 0.2 - - - -
25K ASN* 1.3 78.3 - - - +
27K ALA* 1.3 59.4 + - - +
29K TYR* 3.2 7.5 + - - +
30K ILE* 3.0 34.5 + - - +
32N TRP* 5.4 2.5 - - + -
36N MET* 3.7 26.3 - - + +
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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
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23K THR 2.7 20.2 + - - +
24K CYS* 3.2 9.4 + - - +
26K ALA* 1.3 75.3 - - - +
28K ARG* 1.3 61.8 + - + +
30K ILE* 3.1 15.4 + - - +
31K LEU* 3.2 25.0 + - + +
59K MET* 3.7 32.5 - - + -
87K ILE* 5.3 9.6 - - + -
32N TRP* 4.6 6.7 - - + -
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Residues in contact with ARG 28 (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 CYS* 2.7 34.9 + - + +
25K ASN* 4.2 9.7 + - - +
27K ALA* 1.3 73.9 - - + +
29K TYR* 1.3 56.4 + - - +
31K LEU* 3.7 6.5 + - - +
32K ASN* 2.7 41.6 + - - +
87K ILE* 5.9 4.3 - - + +
92K GLY* 3.4 36.1 + - - +
93K LEU* 5.0 9.9 - - - +
94K LEU 5.7 0.4 - - - +
109K ILE* 3.3 32.9 + - - +
110K ASN* 4.0 18.8 + - - +
112K ALA* 5.0 5.8 - - - +
113K ILE 5.9 0.6 - - - +
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Residues in contact with TYR 29 (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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25K ASN 3.1 20.0 + - - +
26K ALA* 3.5 9.6 - - - +
27K ALA 3.2 0.4 - - - -
28K ARG* 1.3 75.3 - - - +
30K ILE* 1.3 64.3 + - - +
32K ASN* 4.4 4.9 - - + +
33K HIS* 3.1 57.5 + + - +
36N MET* 5.1 9.0 - - - -
39N ALA* 3.2 36.8 + - + -
40N LYS* 3.9 24.4 + - + +
42N THR 5.5 0.2 + - - -
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Residues in contact with ILE 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 ALA 3.0 16.8 + - - +
27K ALA* 3.1 8.7 + - - +
29K TYR* 1.3 76.1 - - - +
31K LEU* 1.3 70.5 + - + +
33K HIS 3.0 11.6 + - - -
34K SER* 2.3 35.0 + - - +
43K THR* 5.1 9.2 - - + -
32N TRP* 3.8 39.7 - - + +
35N LEU* 4.6 18.4 - - + +
36N MET* 3.8 26.7 - - + -
39N ALA* 4.0 22.9 - - + -
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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
----------------------------------------------------------
27K ALA* 3.2 21.4 + - + +
28K ARG* 4.2 6.7 - - - +
29K TYR 3.5 0.2 - - - -
30K ILE* 1.3 88.5 - - + +
32K ASN* 1.3 63.0 + - - +
33K HIS 3.6 0.5 + - - -
34K SER* 3.9 11.6 + - - +
39K LYS* 3.7 35.3 + - + +
43K THR* 4.4 16.4 - - + +
59K MET* 6.0 7.2 - - + -
87K ILE* 6.3 3.1 - - + -
88K ASN 5.7 0.2 - - - +
89K SER* 3.3 43.7 - - - +
92K GLY* 6.1 4.0 - - - +
45N GLN* 4.4 7.4 - - - +
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Residues in contact with ASN 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K ARG* 2.7 27.3 + - - +
29K TYR* 4.4 3.0 - - - +
30K ILE 3.2 0.8 - - - -
31K LEU* 1.3 81.5 - - - +
33K HIS* 1.3 66.1 + - + +
34K SER 3.7 0.7 - - - -
44N LEU* 3.4 24.8 - - + +
45N GLN* 2.6 39.7 + - - +
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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
------------------------------------------------------------
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