Contacts of the helix formed by residues 71 - 79 (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 ALA 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.1 47.5 + - + -
69B GLY 3.3 1.2 + - - -
70B MET* 1.3 78.7 - - - +
72B ILE* 1.3 63.2 + - - +
73B ALA 3.3 2.0 - - - -
74B ALA* 3.8 10.3 - - + +
75B SER* 2.8 39.4 + - - +
97B ARG* 5.3 0.4 - - - +
101B TRP* 4.3 9.0 - - + +
4002B SAH 3.3 0.2 + - - -
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Residues in contact with ILE 72 (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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218A ASP* 5.3 0.4 - - - +
43B ARG* 3.9 27.4 - - + -
46B THR* 3.9 34.8 - - + +
49B MET* 3.6 22.9 - - + -
50B HIS* 3.6 18.5 + - - +
70B MET* 3.1 16.5 + - + +
71B ALA* 1.3 78.1 - - - +
73B ALA* 1.3 62.5 + - - +
75B SER* 3.7 4.4 + - - -
76B ARG 3.6 6.4 + - - -
4002B SAH 3.3 20.4 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B MET* 3.5 37.9 - - + +
53B ALA* 3.3 12.6 - - + +
65B GLU* 4.1 10.3 - - - +
72B ILE* 1.3 73.9 - - - +
74B ALA* 1.3 66.6 + - - +
75B SER 3.0 1.6 - - - -
76B ARG* 2.9 3.7 + - - -
77B VAL* 2.9 22.0 + - - +
132B LEU* 4.4 10.3 - - + -
4002B SAH 3.0 20.1 + - - +
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Residues in contact with ALA 74 (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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65B GLU* 3.3 32.9 + - - +
68B PHE* 3.8 30.3 - - + -
71B ALA* 3.6 8.6 + - - +
72B ILE 3.5 0.2 - - - -
73B ALA* 1.3 78.9 - - - +
75B SER* 1.3 57.2 + - - +
77B VAL* 3.9 0.7 - - - -
78B GLN 3.2 18.9 + - - -
85B HIS* 3.4 12.4 - - + -
87B ILE* 5.7 0.7 - - + -
101B TRP* 3.5 16.7 - - + -
4002B SAH 5.3 0.2 - - - -
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Residues in contact with SER 75 (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* 6.0 0.4 - - - -
71B ALA* 2.8 26.1 + - - +
72B ILE* 3.9 4.9 - - - -
74B ALA* 1.3 75.4 - - - +
76B ARG* 1.3 64.7 + - - +
78B GLN* 3.4 6.2 + - - +
79B GLN* 3.3 22.8 + - - +
101B TRP* 3.7 24.0 + - - -
105B GLN* 5.4 1.1 - - - +
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Residues in contact with ARG 76 (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* 3.4 48.5 + - + +
53B ALA* 3.6 15.9 - - + -
54B ALA* 3.8 26.1 - - - +
72B ILE 3.6 2.2 + - - -
73B ALA 2.9 7.9 + - - +
75B SER* 1.3 74.9 - - - +
77B VAL* 1.3 65.6 + - - +
79B GLN* 3.0 48.7 + - - +
80B ALA* 4.1 13.3 - - - +
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Residues in contact with VAL 77 (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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53B ALA* 3.4 30.7 - - + +
56B ALA* 5.1 0.4 - - + -
57B ALA* 4.5 9.2 - - + -
63B VAL* 4.1 19.7 - - + -
65B GLU* 4.3 6.1 - - - +
73B ALA 2.9 19.6 + - - +
74B ALA 3.7 1.6 - - - +
76B ARG* 1.3 80.2 - - - +
78B GLN* 1.3 62.6 + - - +
79B GLN 3.1 1.0 + - - -
80B ALA* 3.1 21.1 + - - +
82B ILE* 4.2 9.7 - - + +
85B HIS* 3.4 37.2 - - + +
132B LEU* 4.2 12.6 - - + -
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Residues in contact with GLN 78 (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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74B ALA 3.2 4.8 + - - +
75B SER* 3.5 10.8 - - - +
76B ARG 3.2 0.4 - - - -
77B VAL* 1.3 79.1 - - - +
79B GLN* 1.3 57.7 + - - +
80B ALA 3.2 0.4 - - - -
82B ILE* 5.2 1.3 - - - -
85B HIS* 3.3 16.2 + - - +
101B TRP* 3.5 19.3 - - + -
105B GLN* 3.3 32.8 - - - +
106B PRO* 3.0 18.8 - - + +
107B HIS* 2.9 91.0 + - - +
109B VAL* 3.3 11.1 - - - +
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Residues in contact with GLN 79 (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* 5.3 4.7 + - - -
75B SER 3.3 11.9 + - - +
76B ARG* 3.0 56.7 + - - +
78B GLN* 1.3 79.2 - - - +
80B ALA* 1.3 56.2 + - - +
81B PRO* 4.9 0.2 - - - +
106B PRO* 5.5 0.9 - - - -
107B HIS* 5.1 0.7 - - - -
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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