Contacts of the helix formed by residues 48 - 57 (chain B) in PDB entry 1P4D
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 ASP 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B TRP* 4.3 4.2 - - - +
46B SER 3.9 3.6 + - - -
47B VAL* 1.3 70.7 - - - +
49B LYS* 1.3 60.1 + - - +
50B ASP* 3.0 20.1 + - - +
51B VAL* 2.9 45.2 + - + +
52B PHE* 2.8 30.1 + - - +
54B ARG* 4.7 0.5 + - - -
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Residues in contact with LYS 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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14B GLY* 4.0 14.8 - - - +
15B ASN* 3.4 26.4 + - - +
18B THR* 3.2 35.3 + - + +
47B VAL 3.3 6.5 + - - +
48B ASP* 1.3 72.1 + - - +
50B ASP* 1.3 66.0 + - - +
52B PHE* 3.4 7.1 + - - +
53B THR* 2.9 35.7 + - + +
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Residues in contact with ASP 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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48B ASP* 3.0 14.5 + - - +
49B LYS* 1.3 86.4 - - - +
51B VAL* 1.3 62.1 + - - +
53B THR* 2.5 26.1 + - - +
54B ARG* 3.0 28.9 + - - +
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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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33B TRP* 4.5 15.5 - - + -
43B LEU* 4.6 16.4 - - + -
48B ASP* 2.9 39.2 + - + +
50B ASP* 1.3 72.7 - - - +
52B PHE* 1.3 57.5 + - - +
54B ARG* 3.3 27.9 + - + +
55B LEU* 2.9 29.4 + - + +
59B ARG 6.1 0.4 - - - +
61B PRO* 4.9 19.5 - - + -
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Residues in contact with PHE 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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13B ALA 4.2 7.6 - - - -
14B GLY* 4.2 15.0 - - - -
17B TYR* 4.2 16.2 - + + -
18B THR* 5.3 1.8 - - + -
33B TRP* 4.1 15.2 - + - -
47B VAL* 3.9 11.4 - - + -
48B ASP 2.8 17.1 + - - +
49B LYS* 3.5 8.5 - - - +
51B VAL* 1.3 78.6 - - - +
53B THR* 1.3 62.2 + - - +
55B LEU* 3.4 8.8 - - + +
56B LEU* 3.2 51.4 + - + +
142B ALA* 3.4 29.4 - - + -
144B PHE* 3.7 23.1 - + - -
161B VAL* 3.7 24.9 - - + -
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Residues in contact with THR 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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10B ALA* 3.3 31.6 - - - +
11B GLY 5.5 1.8 - - - +
14B GLY* 4.1 22.2 - - - -
49B LYS* 2.9 25.6 - - + +
50B ASP* 2.5 23.2 + - - +
52B PHE* 1.3 74.6 - - - +
54B ARG* 1.3 68.5 + - - +
56B LEU* 3.1 12.0 + - - +
57B GLU* 3.1 17.8 + - - +
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Residues in contact with ARG 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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48B ASP* 4.7 0.2 + - - -
50B ASP* 3.0 33.1 + - - +
51B VAL* 3.5 29.1 - - + +
53B THR* 1.3 83.3 + - - +
55B LEU* 1.3 56.1 + - - +
57B GLU* 2.6 41.2 + - - +
58B GLY 2.9 9.0 + - - -
59B ARG* 3.1 27.6 + - + +
61B PRO* 6.3 1.2 - - - +
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Residues in contact with LEU 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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33B TRP* 3.5 33.7 - - + -
41B LEU* 5.2 1.6 - - + -
43B LEU* 5.1 2.7 - - + -
51B VAL* 2.9 15.3 + - + +
52B PHE* 3.4 18.2 - - + +
54B ARG* 1.3 77.2 - - - +
56B LEU* 1.3 59.2 + - + +
58B GLY* 3.1 17.0 + - - +
59B ARG 3.5 11.1 + - - +
60B LEU* 3.3 26.1 - - + +
61B PRO* 5.7 3.6 - - + -
76B HIS* 4.7 3.3 - - - -
140B VAL* 3.9 22.7 - - + +
141B MET 6.0 0.2 - - - -
142B ALA* 5.8 0.4 - - + -
163B ALA* 3.7 30.3 - - + +
165B VAL* 4.4 4.9 - - + +
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Residues in contact with LEU 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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7B VAL* 4.2 8.5 - - + -
10B ALA* 3.5 25.0 - - + +
13B ALA* 3.5 32.1 - - + -
52B PHE* 3.2 37.0 + - + +
53B THR* 3.1 3.7 + - - +
54B ARG 3.1 1.2 - - - -
55B LEU* 1.3 75.4 - - + +
57B GLU* 1.3 60.5 + - - +
58B GLY 3.2 0.4 - - - -
74B ASN* 5.0 0.2 + - - -
76B HIS* 3.7 6.6 + - - +
78B PRO* 3.4 49.1 - - + +
161B VAL* 4.2 18.8 - - + -
163B ALA* 4.3 14.1 - - + -
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Residues in contact with GLU 57 (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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10B ALA* 3.3 23.2 - - + +
11B GLY* 5.7 1.6 - - - -
53B THR* 3.1 17.3 + - - +
54B ARG* 2.6 31.0 + - - +
56B LEU* 1.3 73.7 - - - +
58B GLY* 1.3 56.7 + - - +
59B ARG* 3.4 35.4 + - - +
67B SER* 3.5 12.2 - - - -
74B ASN* 2.7 31.7 + - + +
76B HIS* 3.6 4.3 + - - -
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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