Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 4DOH
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 ASN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ALA 5.5 0.7 - - - +
25A LEU* 3.8 13.4 - - + +
37A THR* 1.3 71.3 - - - +
39A LEU* 1.3 64.0 + - - +
40A GLN* 3.1 9.2 + - - +
41A GLU* 3.4 45.0 + - + +
42A ILE* 3.5 18.4 + - + +
119A ILE* 5.7 2.2 - - - +
162B GLN* 5.2 2.2 + - - -
210B LYS* 4.1 18.5 + - - +
211B ALA* 3.7 33.8 - - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 3.6 27.5 - - + +
28A LEU* 5.8 0.2 - - + -
37A THR* 3.2 24.2 + - - +
38A ASN* 1.3 75.7 - - - +
40A GLN* 1.3 63.1 + - - +
42A ILE* 3.2 11.9 + - + +
43A ARG* 3.0 35.0 + - - +
119A ILE* 5.1 0.9 - - + -
169A LEU* 4.2 24.0 - - + +
172A MET* 4.1 22.0 - - + -
173A GLU* 3.3 47.6 - - + +
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 5.4 4.5 - - - +
38A ASN* 3.1 8.4 - - - +
39A LEU* 1.3 74.7 - - - +
41A GLU* 1.3 66.9 + - - +
43A ARG* 3.2 11.6 + - - +
44A ASN* 2.9 62.8 + - - +
184B ARG* 6.2 1.6 - - - +
210B LYS* 4.9 14.4 - - - +
224R GLY* 3.0 42.6 + - - +
226R PRO* 4.2 1.2 - - - +
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASN* 3.4 36.7 + - - +
40A GLN* 1.3 76.4 - - - +
42A ILE* 1.3 63.8 + - + +
44A ASN* 3.4 9.1 + - - +
45A GLY* 3.0 19.2 + - - -
115A SER* 3.4 16.6 + - - +
104B THR* 3.1 25.7 - - - +
105B ALA* 4.4 1.0 - - - -
133B ARG* 3.0 33.5 + - - -
162B GLN* 3.7 15.2 + - - +
210B LYS* 5.8 0.2 - - - +
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASN 3.5 16.6 + - - +
39A LEU* 3.2 9.0 + - + +
40A GLN 3.2 0.6 - - - -
41A GLU* 1.3 76.9 - - + +
43A ARG* 1.3 57.4 + - - +
45A GLY* 3.3 0.7 + - - -
46A PHE* 2.9 27.0 + - - +
112A LEU* 3.5 25.7 - - + +
115A SER* 3.6 32.3 - - - +
116A PHE* 4.1 17.5 - - + -
119A ILE* 4.0 27.1 - - + -
165A LEU* 4.8 0.9 - - + -
169A LEU* 3.7 31.2 - - + -
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.0 22.2 + - - +
40A GLN* 3.7 14.1 - - - +
42A ILE* 1.3 75.0 - - - +
44A ASN* 1.3 58.5 + - - +
46A PHE* 3.2 3.2 + - - +
47A SER* 2.9 32.4 + - - -
166A ASP 4.9 0.4 + - - -
169A LEU* 3.8 33.7 + - + +
170A GLN* 2.9 41.8 + - - +
173A GLU* 3.0 37.6 + - - +
133R LEU* 4.0 9.5 - - - +
224R GLY* 4.3 7.1 - - - -
225R PRO* 3.5 48.3 - - + +
226R PRO* 4.6 1.5 - - - +
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 2.9 51.9 + - - +
41A GLU* 3.7 7.5 - - - +
43A ARG* 1.3 75.4 - - - +
45A GLY* 1.3 62.3 + - - +
47A SER* 3.1 19.4 + - - -
48A GLU* 3.3 15.6 - - - +
108A LYS* 5.6 0.2 - - - -
161B PRO* 6.3 1.4 - - - +
226R PRO* 3.6 16.5 - - - +
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLU 3.0 13.8 + - - -
42A ILE* 3.7 3.6 - - - -
44A ASN* 1.3 76.4 - - - +
46A PHE* 1.3 61.0 + - - +
48A GLU* 3.5 21.3 - - - +
49A ILE* 4.2 2.8 + - - +
108A LYS* 3.7 26.6 - - - +
111A SER* 5.9 4.7 - - - -
112A LEU* 4.4 10.3 - - - -
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Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE 2.9 17.7 + - - +
43A ARG* 3.2 5.1 + - - +
45A GLY* 1.3 73.6 - - - +
47A SER* 1.3 63.0 + - - +
48A GLU 3.0 2.5 - - - -
49A ILE* 3.0 19.6 + - + -
50A ARG* 2.9 62.3 + - + -
53A VAL* 5.2 2.0 - - + -
112A LEU* 4.1 20.4 - - + +
162A LEU* 3.4 29.2 - - + -
163A GLY* 4.0 13.0 - - - -
165A LEU* 3.9 19.3 - - + -
166A ASP* 3.6 28.9 - - + -
169A LEU* 4.7 6.1 - - + -
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG 2.9 14.8 + - - -
44A ASN* 3.1 14.4 + - - -
46A PHE* 1.3 77.3 - - - +
48A GLU* 1.3 64.8 + - - +
49A ILE 3.3 0.9 + - - -
50A ARG* 3.8 37.8 + - - +
51A GLY 5.1 1.0 + - - -
225R PRO* 6.4 0.4 - - - -
226R PRO* 3.8 25.7 - - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASN 3.3 18.7 - - - +
45A GLY 3.5 10.8 - - - +
46A PHE 3.0 0.2 - - - -
47A SER* 1.3 81.9 + - - +
49A ILE* 1.3 64.2 + - + +
52A SER* 5.7 0.5 - - - -
104A TYR* 3.8 28.1 + - + +
108A LYS* 3.8 22.4 + - - +
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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