Contacts of the helix formed by residues 47 - 55 (chain B) in PDB entry 1SOZ
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 TYR 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.2 17.1 - - + +
47A TYR* 4.4 10.0 + - - -
45B ALA* 6.5 0.4 - - + -
46B SER* 1.3 77.2 - - - +
48B ASN* 1.3 65.0 + - - +
49B LEU* 3.1 6.0 + - - +
50B ALA* 3.2 16.8 + - + +
51B VAL* 3.2 10.9 + - - +
154B VAL* 3.8 34.0 - - + +
156B LEU* 4.0 27.1 - - + -
170B GLN* 4.6 9.7 + - + -
208B SER* 4.1 19.7 - - - -
47C TYR* 4.7 7.4 + - - -
152C GLY* 2.8 23.0 + - - +
154C VAL* 3.8 20.3 - - + +
172C ILE* 4.1 13.7 - - + -
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 2.8 17.3 + - - +
47B TYR* 1.3 77.3 - - - +
49B LEU* 1.3 50.9 + - - +
51B VAL* 2.8 13.0 + - - +
52B ARG* 2.7 75.9 + - - +
150C HIS* 3.8 28.3 - - + +
151C ILE* 2.9 33.6 + - - +
152C GLY 4.0 0.2 + - - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER 5.0 2.4 + - - +
47B TYR* 3.1 2.0 - - - -
48B ASN* 1.3 75.7 + - - +
50B ALA* 1.3 66.1 + - - +
51B VAL 2.9 0.7 + - - -
52B ARG* 2.9 37.4 + - - +
53B ARG* 2.9 71.0 + - + +
208B SER 4.7 9.0 - - - +
209B LEU* 5.3 4.3 - - + -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 3.2 11.0 + - + +
49B LEU* 1.3 78.8 - - - +
51B VAL* 1.3 56.6 + - - +
53B ARG* 4.4 1.1 - - - -
54B ALA* 3.0 32.9 + - - +
156B LEU* 3.9 15.9 - - + -
206B VAL* 4.7 2.2 - - + +
207B ASN 3.5 17.9 - - - +
208B SER* 3.1 26.2 + - - +
209B LEU 4.4 2.2 - - - -
210B GLY* 3.7 11.9 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR 3.5 14.1 - - - +
48B ASN* 2.8 21.2 + - - +
50B ALA* 1.3 74.7 - - - +
52B ARG* 1.3 65.8 + - - +
55B ALA* 3.0 38.0 + - + +
56B PRO* 3.6 0.7 - - - +
156B LEU* 4.1 12.8 - - + -
158B ILE* 5.5 2.0 - - - -
166B GLN* 5.6 0.9 - - - +
168B ILE* 3.1 37.7 - - + -
151C ILE* 3.7 25.6 - - + +
152C GLY* 4.0 8.7 - - - -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASN* 2.7 62.7 + - - +
49B LEU* 3.3 41.7 - - - +
51B VAL* 1.3 72.9 - - + +
53B ARG* 1.3 60.9 + - + +
56B PRO* 3.0 28.8 - - - +
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Residues in contact with ARG 53 (chain B).
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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42A MET* 5.2 12.9 - - - +
49B LEU* 2.9 54.3 + - + +
50B ALA 4.0 3.6 - - - +
52B ARG* 1.3 79.9 - - + +
54B ALA* 1.3 57.9 + - - +
56B PRO* 4.1 3.6 - - - +
57B ALA* 5.5 0.9 + - - +
140B THR 4.6 4.2 - - - +
142B PRO* 3.6 26.8 - - + +
209B LEU* 3.0 42.9 + - - +
210B GLY* 4.6 0.9 - - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 3.0 16.8 + - - +
53B ARG* 1.3 76.5 - - - +
55B ALA* 1.3 65.2 + - - +
56B PRO* 3.3 3.4 - - - -
57B ALA* 3.2 19.8 + - - +
58B VAL* 3.9 4.0 - - - +
141B ILE* 3.7 18.2 - - + +
142B PRO* 3.9 4.7 - - - -
158B ILE* 4.2 7.0 - - + -
206B VAL* 3.8 13.9 - - + -
210B GLY 3.4 23.8 - - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.0 30.9 + - + +
54B ALA* 1.3 71.1 - - - +
56B PRO* 1.3 70.6 - - + +
57B ALA 3.0 3.3 + - - -
58B VAL* 3.0 11.2 + - - +
109B GLN* 4.5 1.6 - - - +
158B ILE* 3.9 21.1 - - + +
166B GLN* 3.1 41.5 + - - +
168B ILE* 4.5 1.6 - - + -
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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