Contacts of the helix formed by residues 48 - 62 (chain L) in PDB entry 2WSF
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 48 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45L THR* 6.0 2.7 - - - -
47L VAL* 1.3 96.3 - - - +
49L PRO* 1.4 78.3 - - + +
50L LEU* 3.2 18.5 + - + +
52L ARG* 3.6 8.3 - - - +
112L PRO* 6.1 1.0 - - - +
113L SER* 4.4 4.4 - - - +
114L ILE 3.8 11.9 + - - +
115L ALA* 3.3 34.3 - - + +
131L GLN* 6.0 0.2 - - - +
134L ASP 5.2 0.9 - - - +
135L GLY* 5.2 0.7 - - - -
138L LYS* 3.5 27.3 + - - +
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Residues in contact with PRO 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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48L ASN* 1.4 100.3 - - + +
50L LEU* 1.3 66.9 + - - +
51L LEU 3.5 0.4 - - - -
52L ARG* 3.5 9.3 + - + -
53L GLY 3.3 15.9 + - - -
131L GLN* 3.2 33.0 - - + +
135L GLY* 3.2 28.9 - - - +
138L LYS* 3.9 2.9 - - + -
139L PHE* 3.3 30.5 - - + -
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Residues in contact with LEU 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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38H LYS* 6.4 1.8 - - + -
47L VAL* 3.9 13.2 - - + -
48L ASN* 3.2 36.0 - - + +
49L PRO* 1.3 83.7 - - - +
51L LEU* 1.3 95.4 + - + +
53L GLY* 3.5 7.1 + - - -
54L VAL* 5.0 1.2 - - - +
115L ALA* 4.9 6.3 - - + -
138L LYS* 3.0 44.4 - - + +
142L GLY* 4.3 5.2 - - - -
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Residues in contact with LEU 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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33H ASN* 5.7 8.5 - - - +
36H GLN* 3.8 23.1 - - - +
37H SER* 3.6 27.6 - - - -
38H LYS 4.7 4.7 - - - +
40H PHE* 3.9 31.9 - - + -
47L VAL* 4.5 9.6 - - + -
50L LEU* 1.3 112.1 - - + +
52L ARG* 1.3 67.1 + - - +
53L GLY 2.7 6.5 + - - -
54L VAL* 2.9 21.0 + - + +
55L GLU* 3.9 4.9 + - - +
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Residues in contact with ARG 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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32H TYR* 4.9 0.2 - - - -
33H ASN* 5.9 4.7 + - - +
38L SER 4.8 1.4 + - - -
39L ASN 2.4 32.5 + - - -
40L LEU* 3.0 25.7 + - - +
41L PRO* 3.7 25.3 - - + +
44L ARG 3.5 4.4 + - - -
45L THR* 3.2 16.8 - - - +
46L ALA* 2.8 44.2 - - - +
47L VAL* 4.2 8.5 + - + +
48L ASN 3.6 20.4 + - - +
49L PRO* 3.5 8.7 + - - +
51L LEU* 1.3 75.2 - - - +
53L GLY* 1.3 63.2 + - - +
54L VAL 3.1 0.5 + - - -
55L GLU* 3.3 11.1 + - - +
56L VAL* 2.9 33.1 + - + +
139L PHE* 3.9 9.4 - - + -
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Residues in contact with GLY 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 PRO 3.3 6.5 + - - -
50L LEU 3.8 9.2 - - - -
51L LEU 2.7 3.0 + - - -
52L ARG* 1.3 78.2 - - - +
54L VAL* 1.3 49.3 + - - -
56L VAL* 3.5 3.1 - - - +
57L GLY* 2.5 31.0 + - - -
139L PHE* 3.5 32.8 - - - -
142L GLY* 3.4 12.2 - - - +
143L PHE* 3.8 3.3 + - - +
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Residues in contact with VAL 54 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36H GLN* 5.9 1.3 - - - +
40H PHE* 3.8 35.7 - - + -
50L LEU 5.0 2.0 - - - +
51L LEU* 2.9 18.2 + - + +
53L GLY* 1.3 70.1 - - - -
55L GLU* 1.3 59.5 + - - +
56L VAL 3.0 1.1 - - - -
57L GLY* 3.8 1.6 - - - +
58L LEU* 2.4 50.1 + - + +
142L GLY* 3.3 20.0 - - - +
145L PHE* 3.1 27.1 - - + +
146L GLY* 4.4 1.3 - - - -
208L CLA 5.1 8.5 - - - +
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Residues in contact with GLU 55 (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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33H ASN* 5.4 4.6 - - - +
40L LEU* 3.8 20.2 - - - +
51L LEU 3.9 2.9 + - - +
52L ARG* 3.3 13.1 + - - +
54L VAL* 1.3 80.2 - - - +
56L VAL* 1.3 59.1 + - - +
58L LEU* 4.6 0.9 - - - -
59L ALA* 3.0 31.4 + - - +
208L CLA 2.5 94.1 + - + +
209L CLA 3.5 16.3 - - - +
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Residues in contact with VAL 56 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40L LEU* 5.9 1.1 - - + -
41L PRO* 5.7 5.2 - - + -
52L ARG* 2.9 34.5 + - + +
53L GLY 3.5 4.7 - - - +
55L GLU* 1.3 78.8 - - + +
57L GLY* 1.3 67.0 + - - +
60L HIS* 3.2 33.5 + - + +
139L PHE* 3.7 29.8 - - + -
143L PHE* 4.6 9.8 - - + -
209L CLA 2.9 40.2 - - + +
211L BCR 4.6 11.0 - - + -
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Residues in contact with GLY 57 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53L GLY 2.5 22.2 + - - -
54L VAL 3.2 1.1 + - - -
56L VAL* 1.3 74.4 - - - +
58L LEU* 1.3 51.6 + - - +
60L HIS* 3.5 2.3 - - - +
61L GLY* 2.6 28.4 + - - -
92L VAL* 5.5 0.2 - - - +
143L PHE* 3.9 19.6 - - - -
146L GLY* 2.9 26.7 - - - +
147L GLY* 3.4 5.3 + - - -
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Residues in contact with LEU 58 (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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54L VAL* 2.4 30.1 + - + +
55L GLU* 5.5 0.7 - - - -
57L GLY* 1.3 67.9 - - - +
59L ALA* 1.3 57.4 + - - +
61L GLY* 2.8 17.4 + - - -
62L PHE* 2.9 23.2 + - + -
146L GLY* 3.0 14.9 + - - +
149L SER* 5.0 3.6 - - - +
150L GLY* 3.5 22.9 - - - +
153L TRP* 3.0 48.0 - - + +
208L CLA 4.1 28.5 - - + -
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Residues in contact with ALA 59 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L GLU 3.0 21.4 + - - +
58L LEU* 1.3 80.0 - - - +
60L HIS* 1.3 61.1 + - - +
62L PHE* 4.0 14.2 + - - -
63L LEU* 3.9 13.2 + - - +
208L CLA 3.6 39.3 - - + +
209L CLA 3.7 25.6 - - + +
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Residues in contact with HIS 60 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56L VAL* 3.2 18.7 + - + +
57L GLY* 3.5 3.1 - - - +
59L ALA* 1.3 76.1 - - - +
61L GLY* 1.3 67.6 + - - +
63L LEU* 3.3 18.1 - - - +
64L LEU* 3.9 13.2 - - - +
92L VAL* 5.7 1.1 - - - +
143L PHE* 5.0 11.4 - + + -
203L CLA 3.0 24.7 - - + +
209L CLA 2.6 112.0 + + + +
211L BCR 4.8 7.0 - - + +
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Residues in contact with GLY 61 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57L GLY 2.6 21.5 + - - -
58L LEU 2.8 8.6 + - - -
60L HIS* 1.3 74.1 - - - +
62L PHE* 1.3 52.9 + - - -
63L LEU 2.5 25.9 + - - +
64L LEU* 4.5 3.6 - - - +
92L VAL* 5.2 3.1 - - - -
146L GLY 3.8 9.4 - - - -
147L GLY* 4.5 7.4 - - - -
150L GLY 3.3 9.9 - - - -
151L VAL* 4.3 11.2 - - - +
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Residues in contact with PHE 62 (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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58L LEU* 2.9 21.9 + - + -
59L ALA* 4.1 16.2 - - - -
61L GLY* 1.3 65.7 - - - -
63L LEU* 1.3 65.7 + - - +
65L VAL* 3.4 13.7 - - - +
150L GLY 2.8 20.6 + - - +
151L VAL* 4.8 0.4 - - - +
153L TRP* 4.0 35.4 - + + -
154L ALA* 3.7 24.6 - - + +
157L LEU* 6.1 1.3 - - + -
208L CLA 5.3 13.5 - + + -
210L CLA 3.8 63.3 + + + -
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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