Contacts of the helix formed by residues 35 - 41 (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 GLY 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ALA* 1.3 77.7 - - - +
36B ARG* 1.3 66.6 + - - -
37B GLY 3.2 2.7 - - - -
38B ALA* 3.2 9.2 + - - +
39B GLU* 3.3 11.8 + - - +
44B GLN* 5.6 0.2 - - - +
118B GLU* 3.2 15.5 - - - -
139B LEU 3.3 6.1 - - - -
141B MET* 3.7 13.9 - - - +
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Residues in contact with ARG 36 (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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101A ARG* 5.7 8.6 - - - +
211A LEU 5.4 1.0 + - - -
292A ARG* 6.1 2.2 - - - +
296A ASP* 3.2 54.8 + - - +
299A ALA* 4.7 6.3 - - - +
300A ASP* 2.5 45.0 + - - -
35B GLY* 1.3 69.8 - - - -
37B GLY* 1.3 63.3 + - - +
39B GLU* 3.3 10.4 + - - +
40B GLN* 3.1 22.0 + - - +
115B ARG* 5.7 5.2 + - - +
118B GLU* 2.5 38.2 + - - +
137B GLY* 2.9 25.4 + - - -
138B ASN* 3.8 13.2 - - + -
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Residues in contact with GLY 37 (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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36B ARG* 1.3 81.3 - - - +
38B ALA* 1.3 62.4 + - - +
40B GLN* 3.2 13.5 + - - +
41B LEU* 3.2 18.2 + - - +
138B ASN* 3.8 15.0 - - - +
139B LEU 2.7 21.4 + - - +
140B VAL* 3.9 11.7 - - - -
172B TRP* 3.9 6.5 - - - -
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Residues in contact with ALA 38 (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* 4.3 4.9 - - + -
34B ALA* 3.0 37.7 - - - +
35B GLY 3.2 5.4 + - - +
37B GLY* 1.3 76.1 - - - +
39B GLU* 1.3 63.3 + - - +
41B LEU* 3.0 9.5 + - - +
43B LEU* 3.0 37.9 + - + +
44B GLN* 5.1 0.9 - - - +
139B LEU 3.2 5.1 + - - -
140B VAL* 3.9 19.2 - - + +
141B MET 4.5 0.9 - - - +
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Residues in contact with GLU 39 (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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98A GLY 3.6 9.7 - - - +
99A ASP* 5.1 0.9 - - - +
100A LYS 5.5 0.7 + - - -
101A ARG* 4.9 6.8 + - - -
292A ARG* 2.9 43.1 + - - -
35B GLY 3.3 8.6 + - - +
36B ARG* 3.7 11.5 - - - +
37B GLY 3.3 0.4 - - - -
38B ALA* 1.3 79.2 - - - +
40B GLN* 1.3 56.8 + - - +
42B GLY* 2.9 20.5 + - - +
43B LEU 4.0 6.9 + - - -
44B GLN* 2.9 33.8 + - + +
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Residues in contact with GLN 40 (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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289A ARG* 5.7 7.7 - - - +
36B ARG 3.1 12.4 + - - +
37B GLY* 3.4 13.9 - - - +
38B ALA 3.2 0.2 - - - -
39B GLU* 1.3 77.2 - - - +
41B LEU* 1.3 59.1 + - + +
42B GLY 3.0 3.2 + - - -
167B GLN* 3.3 34.1 + - - +
172B TRP* 4.7 4.9 - - + -
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Residues in contact with LEU 41 (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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37B GLY 3.2 9.6 + - - +
38B ALA 3.0 7.6 + - - +
40B GLN* 1.3 74.9 - - - +
42B GLY* 1.3 62.4 + - - +
43B LEU* 3.2 16.0 + - + +
55B LEU* 5.2 0.4 - - + -
60B LEU* 4.1 13.5 - - + -
61B PRO* 3.6 35.8 - - + +
62B ASP* 3.4 32.5 - - + +
140B VAL* 4.0 24.2 - - + -
172B TRP* 3.3 36.8 - - + -
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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