Contacts of the helix formed by residues 45 - 57 (chain B) in PDB entry 1P1B
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 GLU 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.7 17.0 + - - +
43B ARG* 3.4 17.5 - - + +
44B TRP* 1.3 122.1 + - + +
46B THR* 1.3 66.7 + - - +
47B PRO* 3.3 3.4 - - - -
48B TYR* 2.9 13.7 + - + +
49B MET* 2.8 27.1 + - + +
170B LEU* 5.1 7.9 - - + -
213B LEU* 4.2 4.7 - - - -
221B TYR* 2.4 30.3 + - - +
227B MET* 5.8 0.4 - - - -
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Residues in contact with THR 46 (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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43B ARG* 3.0 30.7 + - - +
45B GLU* 1.3 76.9 - - - +
47B PRO* 1.3 73.4 - - + +
49B MET* 2.9 3.3 + - - +
50B HIS* 2.8 56.1 + - + +
72B ILE* 3.9 23.5 - - + +
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Residues in contact with PRO 47 (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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43B ARG 4.5 0.7 - - - +
44B TRP 3.6 12.6 - - - +
45B GLU* 3.4 4.3 - - - -
46B THR* 1.3 99.1 - - + +
48B TYR* 1.3 58.9 + - - +
50B HIS* 3.4 10.7 + - + +
51B SER* 3.2 20.6 + - - -
211B MET* 3.7 22.2 - - + +
213B LEU* 4.5 10.5 - - + -
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Residues in contact with TYR 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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45B GLU* 2.9 11.9 + - + +
47B PRO* 1.3 74.3 - - - +
49B MET* 1.3 72.3 + - - +
50B HIS 3.0 1.6 - - - -
51B SER* 2.9 12.9 + - - +
52B LEU* 3.1 42.6 + - + +
167B TYR 4.0 0.3 + - - -
168B CYS* 3.3 20.8 - - + +
170B LEU* 3.7 29.4 - - + -
173B TRP* 3.6 4.2 - - - -
211B MET* 4.0 13.1 - - - +
213B LEU* 4.2 17.4 - - + +
227B MET* 3.4 38.4 - - + -
228B ILE 2.7 24.8 + - - -
229B THR* 3.4 24.0 - - - -
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Residues in contact with MET 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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220A ARG* 3.5 21.3 - - - +
45B GLU* 2.8 20.6 + - + +
46B THR* 3.3 8.7 - - - +
48B TYR* 1.3 83.7 - - - +
50B HIS* 1.3 61.7 + - - +
52B LEU* 3.6 20.1 + - + +
53B ALA* 3.2 16.1 + - - +
72B ILE* 3.6 24.5 - - + -
73B ALA* 3.5 23.1 - - + +
132B LEU* 5.7 0.7 - - + -
134B ASP* 2.6 32.5 - - + +
4002B SAH 2.9 35.2 - - - +
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Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 2.8 37.8 + - + +
47B PRO* 3.5 12.4 - - + +
48B TYR 3.0 0.2 - - - -
49B MET* 1.3 78.2 - - - +
51B SER* 1.3 59.9 + - - +
53B ALA* 3.6 1.2 - - - +
54B ALA* 2.9 30.0 + - - +
72B ILE* 3.6 21.3 + - + +
75B SER* 6.0 0.4 - - - -
76B ARG* 3.4 41.3 + - + +
79B GLN* 5.3 4.0 + - - -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PRO 3.2 11.8 + - - -
48B TYR* 2.9 12.4 + - - -
50B HIS* 1.3 74.1 - - - +
52B LEU* 1.3 65.5 + - - +
54B ALA* 3.5 5.7 + - - +
55B ALA* 3.0 24.3 + - - +
209B GLU* 5.3 2.8 + - - +
211B MET* 4.4 10.3 - - - -
229B THR* 2.7 32.3 + - - +
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Residues in contact with LEU 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 TYR* 3.1 54.2 + - + +
49B MET* 3.9 29.6 - - + +
51B SER* 1.3 76.4 - - - +
53B ALA* 1.3 56.8 + - - +
55B ALA* 3.3 1.1 + - - -
56B ALA* 2.9 25.3 + - - +
132B LEU* 3.9 22.7 - - + -
134B ASP* 4.8 0.2 - - - +
166B THR* 3.2 31.9 - - + +
167B TYR* 3.6 14.4 - - - +
168B CYS* 4.0 11.4 - - - -
229B THR* 3.9 10.3 - - + -
230B PRO* 4.5 0.4 - - + -
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Residues in contact with ALA 53 (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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49B MET 3.2 14.3 + - - +
50B HIS 3.6 0.2 - - - +
51B SER 3.2 0.2 - - - -
52B LEU* 1.3 77.1 - - - +
54B ALA* 1.3 65.5 + - - +
56B ALA* 3.2 1.6 + - - -
57B ALA* 3.0 26.3 + - - +
73B ALA* 3.3 28.9 - - + +
76B ARG* 3.6 19.3 - - + -
77B VAL* 3.4 18.8 - - + +
132B LEU* 3.7 5.5 - - - +
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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 HIS 2.9 18.1 + - - +
51B SER* 3.9 6.1 - - - +
53B ALA* 1.3 75.6 - - - +
55B ALA* 1.3 57.2 + - - +
57B ALA* 3.2 3.6 + - - -
58B SER* 2.8 29.5 + - - -
76B ARG* 3.8 30.0 - - - +
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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 SER 3.0 19.0 + - - +
52B LEU 3.5 4.9 - - - +
53B ALA 3.1 0.2 - - - -
54B ALA* 1.3 77.0 - - - +
56B ALA* 1.3 59.4 + - - +
58B SER* 2.6 29.5 + - - -
164B ILE* 3.3 11.1 - - + +
166B THR* 4.0 15.5 - - - +
229B THR* 4.4 2.9 - - + -
231B LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 56 (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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52B LEU 2.9 16.9 + - - +
53B ALA 3.2 3.8 + - - +
55B ALA* 1.3 76.8 - - - +
57B ALA* 1.3 58.2 + - - +
58B SER 3.4 0.4 + - - -
59B ARG 4.6 1.4 + - - -
60B GLY 5.3 0.5 - - - +
63B VAL* 3.5 18.7 - - + +
77B VAL* 5.1 0.7 - - + -
129B ASP 4.9 0.3 - - - -
130B GLY* 3.5 21.6 + - - -
131B ILE 3.9 10.3 - - - +
132B LEU* 3.7 30.3 - - + -
164B ILE* 4.0 8.5 - - - +
166B THR* 3.8 9.5 - - + +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA 3.0 17.6 + - - +
54B ALA* 3.5 4.9 - - - +
56B ALA* 1.3 74.8 - - - +
58B SER* 1.3 56.0 + - - +
59B ARG 2.8 13.1 + - - -
60B GLY* 2.9 13.1 + - - -
63B VAL* 4.2 0.4 - - - -
77B VAL* 4.4 11.7 - - + +
80B ALA* 3.6 22.7 - - + +
81B PRO* 5.3 2.8 - - - +
82B ILE* 3.3 29.4 - - + +
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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
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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