Contacts of the helix formed by residues 37 - 54 (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 37 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385K TYR* 4.6 13.1 - - - -
33L LEU 3.5 3.1 + - - -
34L LEU* 3.5 7.9 + - - -
35L GLN 3.5 3.6 + - - -
36L GLU* 1.3 79.5 - - - +
38L TRP* 1.3 63.6 + - - +
39L VAL* 3.3 2.7 - - - -
40L ASP* 3.3 15.2 + - - +
41L LYS* 3.0 26.0 + - - +
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Residues in contact with TRP 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LEU* 2.8 45.7 + - + +
36L GLU* 3.3 23.9 - - + +
37L GLY* 1.3 74.8 - - - +
39L VAL* 1.3 73.0 + - + +
41L LYS* 3.3 20.9 + - - +
42L VAL* 3.2 48.0 + - + +
69L ALA* 3.8 21.3 - - + -
72L MET* 3.4 35.7 + - + +
73L VAL* 3.8 15.6 - - + +
20M LEU* 5.7 3.1 - - + -
23M LEU* 3.6 32.1 - - + -
24M ILE* 4.4 14.8 - - + -
27M ILE* 4.9 2.9 - - + -
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Residues in contact with VAL 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K TYR* 5.6 0.9 - - - +
468K ARG* 4.9 12.3 - - - +
30L LYS* 5.7 1.3 - - - +
33L LEU* 3.8 11.4 + - + +
34L LEU* 4.1 27.6 - - + +
37L GLY* 3.3 0.8 - - - -
38L TRP* 1.3 87.0 - - + +
40L ASP* 1.3 63.0 + - - +
42L VAL* 3.1 21.1 - - - +
43L LYS* 3.2 34.5 + - + +
23M LEU* 6.4 0.4 - - + -
27M ILE* 4.3 17.0 - - + -
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Residues in contact with ASP 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385K TYR* 5.3 8.8 + - + +
437K GLY* 6.2 1.5 - - - -
452K GLN* 3.1 29.8 + - - +
37L GLY* 3.3 16.6 + - - +
38L TRP 3.2 0.4 - - - -
39L VAL* 1.3 80.1 - - - +
41L LYS* 1.3 57.7 + - + +
43L LYS* 3.2 10.0 + - - +
44L ASP* 2.7 41.9 + - - +
47L LYS* 5.4 0.3 + - - -
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Residues in contact with LYS 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L GLU* 3.2 21.6 + - - +
37L GLY 3.0 28.0 + - - +
38L TRP* 3.3 25.7 + - + +
40L ASP* 1.3 79.2 - - + +
42L VAL* 1.3 63.5 + - + +
44L ASP* 3.4 13.6 + - - +
45L LEU* 3.3 18.5 + - - +
72L MET* 5.5 12.1 - - + +
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Residues in contact with VAL 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L TRP* 3.3 48.7 - - + +
39L VAL* 3.1 18.2 - - - +
41L LYS* 1.3 77.2 - - + +
43L LYS* 1.3 61.6 + - - +
45L LEU* 3.3 18.1 + - + +
46L THR* 3.3 14.9 + - - +
65L VAL* 5.8 0.7 - - - +
69L ALA* 4.6 7.0 - - + -
72L MET* 3.9 15.9 - - - -
24M ILE* 6.3 0.2 - - + -
27M ILE* 3.8 34.3 - - + +
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Residues in contact with LYS 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436K GLY 6.6 0.4 - - - -
468K ARG* 5.3 3.8 - - - +
39L VAL* 3.2 38.2 + - + +
40L ASP* 3.2 9.4 + - - +
42L VAL* 1.3 76.5 - - - +
44L ASP* 1.3 60.2 + - - +
46L THR* 3.1 22.5 - - + +
47L LYS* 2.6 30.3 + - - +
27M ILE* 3.8 24.0 - - + -
31M GLU* 3.9 23.2 + - - +
67N ASP* 4.9 11.1 + - - -
69N LEU 5.4 2.0 + - - -
70N ASP* 5.2 12.1 - - - +
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Residues in contact with ASP 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L ASP* 2.7 33.9 + - - +
41L LYS* 3.4 17.5 - - - +
42L VAL 3.3 0.4 - - - -
43L LYS* 1.3 76.0 - - - +
45L LEU* 1.3 59.4 + - - +
47L LYS* 3.2 30.8 + - + +
48L SER* 2.9 17.3 + - - -
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L LYS 3.3 11.4 + - - +
42L VAL* 3.5 12.8 - - + +
43L LYS 3.2 0.6 - - - -
44L ASP* 1.3 79.3 - - - +
46L THR* 1.3 57.7 + - - +
48L SER* 2.6 22.1 + - - +
49L GLU* 3.0 32.3 + - - +
65L VAL* 3.8 31.6 - - + +
68L LYS* 4.0 31.4 - - + +
69L ALA* 5.1 2.9 - - + +
72L MET* 4.6 15.0 - - + -
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Residues in contact with THR 46 (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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42L VAL 3.3 10.9 + - - +
43L LYS* 3.1 23.6 - - - +
45L LEU* 1.3 76.0 - - - +
47L LYS* 1.3 66.6 + - + +
49L GLU* 3.1 18.6 + - - +
50L MET* 3.2 21.4 + - - +
61L ILE* 4.5 5.2 - - - +
65L VAL* 4.6 9.6 - - - -
27M ILE* 5.5 2.7 - - + -
28M VAL* 4.3 18.3 - - - +
31M GLU* 3.8 36.7 - - + +
32M THR 5.5 0.2 + - - -
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Residues in contact with LYS 47 (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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436K GLY 4.7 15.1 + - - -
40L ASP* 5.4 0.6 + - - -
43L LYS* 2.6 36.7 + - - +
44L ASP* 3.2 34.4 + - + +
46L THR* 1.3 82.0 - - + +
48L SER* 1.3 60.4 + - - +
50L MET* 3.6 9.4 + - - +
51L ASN* 3.0 28.1 + - - +
31M GLU* 5.6 6.3 + - - +
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Residues in contact with SER 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L ASP 2.9 15.6 + - - -
45L LEU* 2.6 30.7 + - - +
47L LYS* 1.3 77.5 - - - +
49L GLU* 1.3 63.2 + - - +
51L ASN* 3.2 20.1 + - - +
52L ILE* 3.2 22.1 + - - +
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Residues in contact with GLU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU* 3.0 31.4 + - + +
46L THR* 3.1 10.5 + - - +
48L SER* 1.3 77.4 - - - +
50L MET* 1.3 56.6 + - - +
52L ILE* 3.3 18.1 - - - +
53L ASN* 2.7 67.0 + - - +
61L ILE* 3.9 15.7 - - + -
64L THR* 3.4 25.6 + - - +
65L VAL* 3.8 20.6 - - + +
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Residues in contact with MET 50 (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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46L THR* 3.2 22.6 + - - +
47L LYS* 4.0 9.2 - - - +
48L SER 3.3 0.4 - - - -
49L GLU* 1.3 75.8 - - - +
51L ASN* 1.3 62.3 + - - +
54L GLU* 3.1 24.9 + - - +
55L SER 3.5 26.6 + - - +
56L THR* 3.9 27.6 - - + +
61L ILE* 3.9 22.9 - - - -
31M GLU 5.3 1.1 - - - +
32M THR* 4.4 13.5 - - - +
35M GLN* 4.2 31.6 - - + -
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Residues in contact with ASN 51 (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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47L LYS* 3.0 19.3 + - - +
48L SER* 3.2 13.4 + - - +
49L GLU 3.1 1.0 - - - -
50L MET* 1.3 83.5 + - - +
52L ILE* 1.3 61.4 + - + +
54L GLU* 2.8 24.7 - - - +
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Residues in contact with ILE 52 (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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48L SER* 3.2 19.7 - - - +
49L GLU* 3.3 30.5 - - - +
51L ASN* 1.3 78.3 - - + +
53L ASN* 1.3 71.2 + - - +
54L GLU* 2.9 16.1 - - - +
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Residues in contact with ASN 53 (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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49L GLU* 2.7 45.2 + - - +
52L ILE* 1.3 84.5 - - - +
54L GLU* 1.3 75.9 + - - +
55L SER* 3.3 9.7 + - - +
60L GLN* 3.7 28.1 + - - +
61L ILE* 3.4 20.3 - - + +
64L THR* 4.8 6.7 + - - +
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Residues in contact with GLU 54 (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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50L MET 3.1 17.2 + - - +
51L ASN 2.8 20.2 - - - +
52L ILE* 2.9 26.3 - - - +
53L ASN* 1.3 79.1 - - - +
55L SER* 1.3 57.9 + - - +
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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