Contacts of the helix formed by residues 34 - 52 (chain L) in PDB entry 2WQT
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 34 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 5.6 7.9 + - - +
30L ILE* 3.2 29.5 + - - +
31L GLY* 2.9 8.8 + - - +
32L ILE 3.6 0.4 - - - -
33L ASP* 1.3 73.5 - - - +
35L ALA* 1.3 64.6 + - - +
36L GLU* 3.7 10.4 + - - +
37L ALA* 3.3 29.5 + - + +
38L ALA 3.3 12.1 + - - -
152L VAL* 3.2 16.1 - - - +
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ASP 3.4 6.7 + - - +
34L ASN* 1.3 70.8 - - - +
36L GLU* 1.3 66.9 + - - +
38L ALA* 3.2 4.1 + - - +
39L TYR* 3.0 35.6 + - + -
151L PHE* 4.0 25.3 - - + -
152L VAL* 4.4 7.2 - - - -
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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
----------------------------------------------------------
34L ASN* 3.3 8.6 + - - +
35L ALA* 1.3 78.8 - - - +
37L ALA* 1.3 55.9 + - - +
39L TYR* 3.5 6.8 + - - +
40L ALA* 3.0 27.4 + - + +
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Residues in contact with ALA 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L THR* 5.7 2.5 - - - +
6L LEU* 4.1 23.6 - - + +
30L ILE* 4.4 10.8 - - + -
34L ASN* 3.3 32.7 + - + +
35L ALA 3.2 0.8 - - - -
36L GLU* 1.3 76.4 - - - +
38L ALA* 1.3 66.8 + - - +
40L ALA* 3.1 9.8 + - - +
41L ILE* 2.9 28.4 + - - +
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Residues in contact with ALA 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ILE* 4.5 6.8 - - + +
34L ASN 3.3 2.6 + - - -
35L ALA* 3.2 9.5 + - - +
37L ALA* 1.3 78.0 - - - +
39L TYR* 1.3 61.4 + - - +
41L ILE* 3.2 2.9 + - - -
42L GLN* 3.1 18.0 + - - +
151L PHE* 5.7 0.2 - - + -
152L VAL* 3.4 42.4 - - + +
155L VAL* 3.8 17.7 - - + -
156L ALA* 3.4 19.2 + - - +
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Residues in contact with TYR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L ALA* 3.0 31.1 + - + +
36L GLU* 3.9 6.1 - - - +
38L ALA* 1.3 77.2 - - - +
40L ALA* 1.3 57.5 + - - +
42L GLN* 3.4 9.7 + - - +
43L HIS* 2.9 29.7 + - - +
77L PRO 4.3 4.5 + - - -
78L ASP* 3.8 11.1 + - - -
79L PHE* 3.3 72.4 + + - -
151L PHE* 4.4 15.4 - + - -
155L VAL* 3.4 23.9 - - + +
210L TRP* 4.5 3.8 - - - -
214L LYS* 4.4 18.8 + - - -
218L LEU* 6.2 1.6 - - + -
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Residues in contact with ALA 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L LEU* 4.0 21.3 - - + -
36L GLU* 3.0 16.5 + - + +
37L ALA* 3.1 9.4 + - - +
39L TYR* 1.3 76.6 - - - +
41L ILE* 1.3 56.3 + - - +
43L HIS* 3.3 8.1 + - - +
44L ILE* 2.8 38.2 + - + +
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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
----------------------------------------------------------
6L LEU* 4.0 23.6 - - + +
9L LEU* 3.9 31.0 - - + -
10L ALA* 3.9 16.6 - - - +
13L LEU* 3.8 27.8 - - + -
26L LEU* 5.0 1.8 - - + -
30L ILE* 4.2 17.9 - - + -
37L ALA 2.9 17.2 + - - +
38L ALA 3.2 6.5 + - - +
40L ALA* 1.3 73.3 - - - +
42L GLN* 1.3 65.9 + - - +
44L ILE* 3.3 9.8 + - - +
45L ASN* 3.2 22.0 + - - +
156L ALA* 3.9 19.3 - - + +
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Residues in contact with GLN 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L ALA 3.1 8.0 + - - +
39L TYR* 3.6 17.8 - - - +
40L ALA 3.4 0.2 - - - -
41L ILE* 1.3 75.7 - - - +
43L HIS* 1.3 58.8 + - - +
45L ASN* 3.2 6.6 + - - +
46L VAL* 2.9 31.4 + - + +
79L PHE* 3.0 39.9 + - - -
81L THR* 3.1 24.6 + - - -
155L VAL* 3.2 26.9 + - - +
156L ALA 3.8 7.6 + - - -
158L ASN* 3.2 35.1 + - + +
159L ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L TYR 2.9 19.0 + - - +
40L ALA* 3.5 9.4 - - - +
42L GLN* 1.3 74.7 - - - +
44L ILE* 1.3 71.1 + - + +
46L VAL* 3.2 8.9 + - - +
47L GLN* 2.8 58.7 + - + +
220L GLU* 4.2 26.4 + - - -
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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
----------------------------------------------------------
3L LYS* 4.8 10.1 - - - -
6L LEU* 4.9 11.4 - - + +
7L GLU* 3.6 42.4 - - + +
10L ALA* 3.8 19.7 - - + -
14L ARG* 4.5 8.7 - - - +
40L ALA* 2.8 38.1 + - + +
41L ILE* 3.5 9.6 - - - +
43L HIS* 1.3 76.9 - - + +
45L ASN* 1.3 57.8 + - - +
47L GLN* 3.3 6.5 + - - +
48L HIS* 2.9 27.9 + - + +
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Residues in contact with ASN 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L ALA* 3.2 26.9 + - - +
13L LEU* 3.9 19.8 - - - +
14L ARG* 2.8 42.8 + - + +
41L ILE* 3.2 12.4 + - - +
42L GLN* 3.7 7.9 - - - +
43L HIS 3.2 0.2 - - - -
44L ILE* 1.3 76.3 - - - +
46L VAL* 1.3 66.1 + - + +
48L HIS* 3.6 4.2 + - - +
49L ASP* 3.2 31.1 + - - +
156L ALA 4.8 3.0 + - - -
158L ASN* 6.6 0.2 - - + -
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Residues in contact with VAL 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L GLN* 2.9 29.0 + - + +
43L HIS* 3.8 9.4 - - - +
45L ASN* 1.3 75.0 - - + +
47L GLN* 1.3 64.4 + - - +
49L ASP* 3.2 3.3 + - - +
50L VAL* 2.9 39.9 + - + +
56L VAL* 4.4 5.2 - - + -
59L ARG* 5.3 2.9 - - - +
81L THR* 3.7 39.5 - - + +
83L PHE* 4.1 23.6 - - + -
158L ASN* 4.6 3.4 - - - +
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Residues in contact with GLN 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L HIS* 2.8 49.4 + - + +
44L ILE* 3.5 7.2 - - - +
46L VAL* 1.3 83.4 - - - +
48L HIS* 1.3 60.1 + - - +
50L VAL* 3.4 18.9 + - - +
51L ALA* 3.1 23.4 + - - +
220L GLU* 5.5 0.9 - - - +
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Residues in contact with HIS 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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14L ARG* 3.7 43.1 + - - +
44L ILE* 2.9 17.7 + - + +
45L ASN* 3.7 9.2 - - - +
47L GLN* 1.3 77.0 - - - +
49L ASP* 1.3 74.0 + - - +
51L ALA* 3.3 14.4 + - - +
52L GLN* 3.3 39.4 + - + +
1264L K 4.3 5.6 - - - -
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Residues in contact with ASP 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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14L ARG* 4.8 2.9 - - - -
45L ASN 3.2 16.5 + - - +
46L VAL 3.2 5.0 + - - +
48L HIS* 1.3 90.3 - - - +
50L VAL* 1.3 64.5 + - - +
52L GLN* 3.0 24.2 + - - +
53L GLY 3.4 0.2 + - - -
54L ARG* 3.0 62.2 + - + +
83L PHE* 4.1 9.3 - - + -
1314L NA 3.4 17.6 - - - -
4T HIS* 3.8 9.5 - - - -
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Residues in contact with VAL 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 VAL* 2.9 26.1 + - + +
47L GLN* 3.8 20.9 - - - +
48L HIS 3.4 0.2 - - - -
49L ASP* 1.3 74.8 - - - +
51L ALA* 1.3 58.3 + - - +
53L GLY* 2.8 22.0 + - - -
54L ARG 3.6 19.0 - - - +
56L VAL* 4.0 24.7 - - + -
83L PHE* 4.3 2.7 - - + -
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Residues in contact with ALA 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 GLN 3.1 13.2 + - - +
48L HIS* 3.4 14.1 - - - +
49L ASP 3.2 0.2 - - - -
50L VAL* 1.3 76.8 - - - +
52L GLN* 1.3 59.5 + - + +
53L GLY 3.3 1.4 + - - -
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Residues in contact with GLN 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L HIS* 3.3 32.4 + - + +
49L ASP* 3.0 21.8 + - - +
51L ALA* 1.3 77.4 - - + +
53L GLY* 1.3 60.0 + - - +
54L ARG* 3.4 2.9 + - + +
1264L K 3.8 19.3 - - - -
3T LYS* 3.1 30.3 + - - +
4T HIS* 4.5 9.3 + - - +
7T GLU* 3.6 40.4 - - + +
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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
------------------------------------------------------------
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