Contacts of the helix formed by residues 37 - 50 (chain L) in PDB entry 6PSS
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 ASP 37 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L ILE* 4.9 1.4 - - - +
36L VAL* 1.3 86.0 + - + +
38L SER* 1.3 79.4 + - - +
39L ASP 3.3 5.2 + - - -
40L GLN* 3.9 12.4 + - - +
41L ILE* 3.4 16.3 - - - +
99L ARG* 2.9 38.3 + - - +
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Residues in contact with SER 38 (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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314J ARG* 4.9 3.1 + - - -
37L ASP* 1.3 81.9 + - - +
39L ASP* 1.3 61.9 + - - +
40L GLN 3.6 0.2 - - - -
41L ILE* 3.8 20.5 - - - +
42L GLU* 3.5 29.6 + - - +
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Residues in contact with ASP 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J GLY 5.3 7.4 - - - +
314J ARG* 3.5 29.2 + - - +
37L ASP* 3.3 4.4 + - - +
38L SER* 1.3 76.4 - - - +
40L GLN* 1.3 71.6 + - + +
42L GLU* 3.3 3.8 + - - +
43L ASP* 2.9 42.9 + - - +
94L THR* 5.4 0.7 - - - +
96L ASP* 2.9 27.9 - - - +
99L ARG* 3.8 17.3 + - - +
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Residues in contact with GLN 40 (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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35L ILE* 4.2 27.0 - - + +
37L ASP* 3.9 10.0 + - - +
39L ASP* 1.3 78.0 + - - +
41L ILE* 1.3 58.0 + - - +
43L ASP* 3.2 12.5 + - - +
44L ILE* 2.9 34.3 + - + +
91L ILE 5.3 4.8 + - - -
92L GLY 6.0 0.2 - - - -
93L ARG 3.4 22.7 + - - +
94L THR* 3.8 24.9 - - - +
99L ARG* 2.9 31.1 + - - +
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Residues in contact with ILE 41 (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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201I ARG* 6.3 0.7 - - - +
28L ASN* 4.1 22.0 - - - +
31L LEU* 4.1 30.3 - - + +
35L ILE* 4.8 16.8 - - + +
36L VAL 4.8 7.4 - - - +
37L ASP 3.4 15.3 - - - +
38L SER* 3.8 25.6 - - - +
40L GLN* 1.3 78.1 - - - +
42L GLU* 1.3 65.5 + - + +
44L ILE* 3.3 14.8 + - + +
45L ILE* 2.9 29.3 + - + +
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Residues in contact with GLU 42 (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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314J ARG* 5.4 9.2 + - - +
24L TYR* 5.8 4.0 - - - -
38L SER* 3.5 22.1 + - - +
39L ASP* 3.3 4.2 + - - +
41L ILE* 1.3 82.9 - - + +
43L ASP* 1.3 60.6 + - - +
44L ILE 3.3 0.2 - - - -
45L ILE* 3.5 26.6 - - + +
46L GLN* 2.9 31.2 + - - +
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Residues in contact with ASP 43 (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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312J ARG* 3.6 37.5 + - - +
313J GLY* 4.9 4.1 - - - -
39L ASP* 2.9 37.6 + - - +
40L GLN* 3.2 14.3 + - - +
42L GLU* 1.3 77.0 - - - +
44L ILE* 1.3 57.0 + - + +
46L GLN* 3.2 11.3 + - - +
47L MET* 2.9 33.4 + - + +
95L THR* 5.4 1.2 + - - -
96L ASP* 5.4 1.9 - - - +
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Residues in contact with ILE 44 (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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133J ARG* 6.3 0.9 - - - +
9L LEU* 4.4 24.7 - - + -
12L LEU* 5.8 1.6 - - + -
27L VAL* 5.2 5.8 - - + -
31L LEU* 4.5 17.3 - - + -
32L PRO* 5.6 3.8 - - + -
35L ILE* 5.8 7.9 - - + -
40L GLN* 2.9 22.6 + - + +
41L ILE* 3.3 17.9 + - + +
43L ASP* 1.3 73.6 - - + +
45L ILE* 1.3 59.6 + - - +
47L MET* 3.2 10.7 + - + +
48L ILE* 2.9 32.1 + - + +
84L LEU* 4.2 23.3 - - + -
87L VAL* 6.5 4.0 - - + -
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Residues in contact with ILE 45 (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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24L TYR* 5.4 7.0 - - + -
27L VAL* 3.7 35.4 - - + -
41L ILE* 2.9 20.3 + - + +
42L GLU* 3.5 28.7 - - + +
43L ASP 3.2 0.2 - - - -
44L ILE* 1.3 76.6 - - - +
46L GLN* 1.3 51.3 + - + +
48L ILE* 3.3 10.6 - - + +
49L ASN* 2.6 54.8 + - - +
55L VAL* 3.7 30.1 - - + +
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Residues in contact with GLN 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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310J GLY 4.5 15.3 + - - -
42L GLU 2.9 17.9 + - - +
43L ASP* 3.5 13.2 - - - +
45L ILE* 1.3 77.1 - - + +
47L MET* 1.3 61.6 + - - +
49L ASN* 3.7 10.5 - - - +
50L ASP* 2.9 40.1 + - - +
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Residues in contact with MET 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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118J LYS* 4.3 20.9 - - - +
120J LEU* 3.8 29.2 - - + -
133J ARG* 5.4 7.2 - - - +
43L ASP* 2.9 21.9 + - + +
44L ILE* 3.4 14.6 - - + +
46L GLN* 1.3 79.7 - - - +
48L ILE* 1.3 56.9 + - - +
50L ASP* 3.0 15.2 - - - +
51L MET* 3.3 19.2 - - - +
80L ALA* 4.4 9.5 - - + +
83L VAL* 3.7 36.3 - - + -
84L LEU* 4.7 15.7 - - + -
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Residues in contact with ILE 48 (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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12L LEU* 5.0 12.1 - - + -
13L VAL* 3.7 34.8 - - + +
22L LEU* 3.7 23.1 - - + -
27L VAL* 5.9 0.4 - - + -
44L ILE* 2.9 17.5 + - + +
45L ILE* 3.3 24.0 - - + +
47L MET* 1.3 75.6 - - - +
49L ASN* 1.3 59.1 + - - +
50L ASP 3.5 0.4 - - - -
51L MET* 3.2 31.3 + - + +
53L ILE* 3.7 24.5 + - + +
55L VAL* 3.7 18.8 - - + +
84L LEU* 4.1 6.7 - - + -
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Residues in contact with ASN 49 (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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45L ILE* 2.6 33.9 + - - +
46L GLN* 3.0 15.3 + - - +
48L ILE* 1.3 77.9 - - - +
50L ASP* 1.3 57.4 + - - +
51L MET 3.2 5.6 - - - -
52L GLY* 3.3 15.1 - - - -
53L ILE 4.9 0.2 - - - +
54L GLN* 4.3 5.9 + - - -
55L VAL* 3.8 34.9 + - + +
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Residues in contact with ASP 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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120J LEU* 3.3 38.4 + - - +
311J ARG* 5.6 3.6 + - - -
46L GLN* 2.9 21.9 + - - +
47L MET* 3.0 18.8 - - - +
49L ASN* 1.3 77.3 - - - +
51L MET* 1.3 63.6 + - - +
52L GLY* 3.5 0.7 - - - -
71L THR 5.2 0.7 - - - +
76L ALA* 5.1 4.9 - - - +
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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