Contacts of the helix formed by residues 20 - 36 (chain L) 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 GLY 20 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37K LYS* 5.8 6.5 - - - -
16L LEU 3.5 1.0 + - - -
17L VAL 3.2 11.7 + - - -
18L GLU 3.1 6.0 + - - -
19L SER* 1.3 78.4 - - - +
21L ASN* 1.3 61.0 + - - +
22L TYR 3.3 2.7 - - - -
23L GLU* 3.1 37.3 - - - +
24L LEU* 3.8 3.7 - - - +
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Residues in contact with ASN 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L TYR* 5.5 1.4 - - - -
16L LEU* 3.1 24.1 + - + +
19L SER* 3.5 24.4 + - - +
20L GLY* 1.3 78.8 - - - +
22L TYR* 1.3 64.7 + - - +
23L GLU 3.3 0.4 - - - -
24L LEU* 3.2 33.3 - - + +
25L ILE* 3.3 14.4 + - - +
88L PHE* 4.6 22.7 + - + +
91L GLU* 3.5 26.2 + - - -
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Residues in contact with TYR 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K PHE* 3.5 49.8 - + - -
52K ILE* 3.2 20.5 + - + +
53K ASN* 2.3 30.9 + - - +
13L GLN* 5.5 6.5 - - + -
16L LEU* 3.0 42.0 + - + +
17L VAL* 3.8 18.6 - - + -
20L GLY 3.3 0.8 - - - -
21L ASN* 1.3 78.3 - - - +
23L GLU* 1.3 58.2 + - - +
25L ILE* 3.1 24.4 - - + +
26L SER* 3.1 15.8 + - - -
15M ILE* 6.0 2.2 - - + -
19M LEU* 3.6 24.8 - - + +
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Residues in contact with GLU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K PRO* 5.8 7.2 - - + -
40K PHE* 5.6 7.6 - - + -
471K ASN* 5.2 0.7 - - - +
20L GLY* 3.1 25.2 - - - +
22L TYR* 1.3 80.2 - - - +
24L LEU* 1.3 77.2 + - - +
26L SER* 2.5 22.0 + - - -
27L ASN* 3.0 44.9 + - - +
50N ASN* 6.0 1.7 - - - -
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Residues in contact with LEU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L GLY 3.8 6.1 - - - +
21L ASN* 3.2 37.7 - - - +
23L GLU* 1.3 94.3 + - - +
25L ILE* 1.3 73.5 + - + +
27L ASN* 3.0 8.4 + - - +
28L GLU* 3.0 41.6 + - - +
84L GLN* 4.8 1.6 - - - +
88L PHE* 3.5 36.3 - - + -
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Residues in contact with ILE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L LEU* 3.8 29.8 - - + -
21L ASN* 3.3 12.3 - - + +
22L TYR* 3.1 29.2 - - + +
24L LEU* 1.3 89.1 - - + +
26L SER* 1.3 59.9 + - - +
28L GLU* 3.2 17.7 - - - +
29L LEU* 3.4 24.6 + - - +
81L VAL* 5.3 5.8 - - + +
85L ILE* 4.3 18.6 - - + -
88L PHE* 3.9 17.9 - - + -
15M ILE* 5.1 7.2 - - + -
19M LEU* 4.4 21.8 - - + +
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Residues in contact with SER 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K PHE* 5.5 4.9 - - - -
22L TYR* 3.1 17.9 + - - -
23L GLU* 2.5 25.3 + - - -
25L ILE* 1.3 81.7 - - - +
27L ASN* 1.3 65.7 + - - +
29L LEU* 3.7 6.1 + - - +
30L LYS* 3.3 39.1 + - - +
19M LEU* 5.2 9.9 - - - -
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Residues in contact with ASN 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469K GLN* 4.4 6.6 + - - +
470K VAL 5.3 0.4 - - - +
471K ASN* 3.3 51.5 + - + +
23L GLU* 3.0 42.2 + - - +
24L LEU* 3.0 9.4 + - - +
26L SER* 1.3 78.4 + - - +
28L GLU* 1.3 61.6 + - - +
30L LYS* 3.3 4.2 + - - +
31L ALA* 3.0 26.7 + - - +
47N ASP 5.5 0.3 - - - +
48N HIS* 4.8 12.3 - - - +
50N ASN* 6.0 2.2 - - - +
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Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471K ASN* 5.1 0.7 - - - +
24L LEU* 3.0 21.4 + - - +
25L ILE* 3.2 31.4 - - - +
27L ASN* 1.3 74.1 - - - +
29L LEU* 1.3 67.6 + - - +
31L ALA* 3.7 8.5 - - - +
32L ARG* 3.2 38.3 + - + +
81L VAL* 5.2 12.0 - - + +
84L GLN* 2.9 45.6 + - - +
85L ILE* 5.5 0.3 - - - +
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Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ILE 3.4 16.6 + - - +
26L SER* 3.9 7.4 - - - +
27L ASN 3.2 0.6 - - - -
28L GLU* 1.3 81.5 - - + +
30L LYS* 1.3 62.3 + - + +
31L ALA 3.5 0.2 + - - -
32L ARG* 4.7 1.3 - - - +
33L LEU* 3.3 36.6 + - + +
77L THR* 6.1 0.4 - - - +
81L VAL* 5.6 14.1 - - + -
16M LEU* 4.7 16.8 - - + -
19M LEU* 3.8 37.0 - - + -
20M LEU* 4.7 9.2 - - + -
23M LEU* 3.9 22.2 - - + -
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Residues in contact with LYS 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469K GLN* 3.8 28.9 - - - +
26L SER* 3.3 25.1 + - - +
27L ASN* 3.3 2.5 + - - +
29L LEU* 1.3 78.0 - - + +
31L ALA* 1.3 63.6 + - - +
33L LEU* 4.0 7.0 - - - +
34L LEU* 3.1 26.9 + - - +
23M LEU* 5.5 16.6 - - + -
47N ASP* 3.2 30.3 + - - -
48N HIS* 4.5 14.1 + - + +
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Residues in contact with ALA 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408K ASP* 4.0 16.8 - - + +
410K ILE* 6.3 3.1 - - + -
469K GLN* 5.0 2.9 - - - -
471K ASN* 3.4 20.4 - - - +
27L ASN 3.0 17.4 + - - +
28L GLU* 3.7 9.6 - - - +
29L LEU 3.3 0.6 - - - -
30L LYS* 1.3 75.1 - - - +
32L ARG* 1.3 69.6 + - + +
34L LEU* 3.3 3.8 + - - +
35L GLN* 3.0 32.0 + - - +
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Residues in contact with ARG 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L GLU* 3.2 22.2 + - + +
29L LEU* 4.7 1.8 - - - +
31L ALA* 1.3 77.7 - - + +
33L LEU* 1.3 62.2 + - + +
35L GLN* 3.6 12.1 + - - +
36L GLU* 3.3 28.0 + - - +
76L SER 5.7 0.2 + - - -
77L THR* 4.3 21.1 - - + +
80L THR* 3.3 45.2 + - - +
81L VAL* 6.3 0.7 - - - -
84L GLN* 5.4 5.9 + - - -
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Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 3.3 38.2 + - + +
30L LYS* 4.2 5.2 - - - +
31L ALA 3.3 0.6 - - - -
32L ARG* 1.3 78.8 - - + +
34L LEU* 1.3 62.0 + - - +
36L GLU* 3.5 18.6 - - - +
37L GLY 3.5 2.3 + - - -
38L TRP* 2.8 78.9 + - + +
39L VAL* 3.8 8.9 + - + -
73L VAL* 4.6 16.4 - - + -
77L THR* 4.6 7.9 - - + -
20M LEU* 5.4 3.8 - - + -
23M LEU* 4.5 13.5 - - + -
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K TYR* 3.2 60.2 - - + +
410K ILE* 4.3 14.4 - - + -
468K ARG* 3.7 49.8 - - + +
469K GLN* 4.1 16.8 - - - +
30L LYS 3.1 19.0 + - - +
31L ALA* 3.3 3.8 + - - +
33L LEU* 1.3 76.5 - - - +
35L GLN* 1.3 64.6 + - + +
36L GLU 3.3 0.7 + - - -
37L GLY* 3.5 3.0 + - - +
38L TRP 5.0 0.2 - - - +
39L VAL* 4.1 21.5 - - + +
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Residues in contact with GLN 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385K TYR* 4.6 13.8 - - + +
387K ASN* 3.8 24.1 - - - +
408K ASP* 3.3 29.6 + - - -
410K ILE* 4.2 20.2 - - + +
31L ALA* 3.0 21.0 + - - +
32L ARG* 3.6 11.7 + - - +
33L LEU 3.4 0.4 - - - -
34L LEU* 1.3 77.2 - - + +
36L GLU* 1.3 57.5 + - - +
37L GLY 3.5 0.4 + - - -
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Residues in contact with GLU 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ARG 3.3 16.3 + - - +
33L LEU* 3.5 31.7 - - - +
35L GLN* 1.3 78.2 - - - +
37L GLY* 1.3 59.8 + - - +
38L TRP* 3.6 15.2 - - + +
41L LYS* 3.2 14.8 + - - +
74L SER* 4.5 11.2 + - - -
76L SER* 5.0 1.9 + - - -
77L THR* 3.6 21.4 + - - +
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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