Contacts of the helix formed by residues 36 - 44 (chain A) in PDB entry 4I6J
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 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 3.4 21.8 + - - -
27A PHE* 3.7 10.9 - - - -
30A GLY* 3.9 8.5 + - - -
32A ARG* 3.0 26.8 + - + +
33A LEU* 3.9 17.9 + - - +
34A HIS 3.3 1.8 - - - +
35A ASP* 1.3 76.4 - - - +
37A PRO* 1.3 59.3 - - - +
38A ALA* 3.6 7.6 + - - +
39A LEU* 2.9 40.7 + - + +
40A LEU* 3.0 15.1 + - - +
117A GLU* 5.3 6.9 - - - +
147A SER* 5.1 1.2 + - - -
185A ALA* 4.5 2.2 - - - +
186A VAL 5.1 1.8 + - - -
188A VAL* 5.3 0.2 - - - +
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Residues in contact with PRO 37 (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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35A ASP* 3.5 16.4 - - - +
36A ASN* 1.3 85.1 - - - +
38A ALA* 1.3 67.2 + - - +
40A LEU* 3.2 18.2 + - + +
41A ALA* 2.9 22.3 + - - +
145A GLU* 3.6 33.1 - - + +
147A SER* 3.9 16.2 - - - +
185A ALA* 4.5 10.7 - - + -
281A ARG* 5.6 2.5 - - - +
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Residues in contact with ALA 38 (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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25A HIS* 3.8 6.7 - - + -
36A ASN* 3.2 8.2 - - - +
37A PRO* 1.3 82.6 - - - +
39A LEU* 1.3 55.9 + - - +
41A ALA* 3.1 8.0 + - - +
42A ALA 2.9 16.1 + - - -
115A THR* 2.7 21.1 + - - -
116A PHE* 3.5 38.6 - - - +
117A GLU* 3.7 6.7 - - + +
143A VAL 4.8 1.3 - - - +
145A GLU* 3.4 16.0 - - + +
147A SER* 5.9 0.2 - - - +
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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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25A HIS* 3.4 38.5 + - + -
33A LEU* 3.9 31.2 - - + +
36A ASN* 2.9 26.0 + - + +
38A ALA* 1.3 74.0 - - - +
40A LEU* 1.3 66.3 + - - +
41A ALA 2.9 2.6 + - - -
42A ALA* 3.1 6.4 + - + +
43A VAL* 3.1 24.1 + - + +
49A VAL* 5.2 1.3 - - + -
51A CYS* 3.8 21.8 - - - -
188A VAL* 3.6 29.2 - - + -
193A MET* 4.6 12.8 - - + -
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Residues in contact with LEU 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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36A ASN 3.0 13.0 + - - +
37A PRO* 3.4 13.7 - - + +
39A LEU* 1.3 74.7 - - - +
41A ALA* 1.3 57.5 + - - +
43A VAL* 3.8 6.8 - - + +
44A ARG* 3.0 30.3 + - - +
185A ALA* 4.4 15.9 - - + -
186A VAL* 3.5 28.7 - - + +
187A ALA 4.4 1.3 - - - +
188A VAL* 3.2 39.7 - - + +
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Residues in contact with ALA 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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37A PRO 2.9 12.4 + - - +
38A ALA* 3.3 11.4 - - - +
39A LEU 2.9 0.2 - - - -
40A LEU* 1.3 74.9 - - - +
42A ALA* 1.3 65.8 + - - +
43A VAL 3.0 2.5 + - - -
44A ARG* 3.6 8.9 - - - +
113A ARG* 3.2 22.2 + - - -
115A THR* 4.2 4.7 - - + -
143A VAL* 4.0 28.5 - - + -
145A GLU* 4.7 3.1 - - - +
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Residues in contact with ALA 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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23A SER* 2.1 38.7 + - - +
25A HIS* 3.9 21.1 - - + +
38A ALA 2.9 7.4 + - - +
39A LEU* 3.6 8.3 - - + +
41A ALA* 1.3 76.5 - - - +
43A VAL* 1.3 61.2 + - - +
46A ALA 5.2 1.4 - - - +
49A VAL* 4.2 9.0 - - + -
113A ARG* 3.5 7.5 + - - +
115A THR* 3.5 31.5 - - + +
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Residues in contact with VAL 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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23A SER* 4.6 0.2 - - - -
39A LEU* 3.1 18.6 + - + +
40A LEU* 3.8 9.6 - - + +
41A ALA 3.0 0.6 - - - -
42A ALA* 1.3 79.5 - - - +
44A ARG* 1.3 56.1 + - - +
45A GLY* 2.6 19.4 + - - -
46A ALA* 3.1 14.0 + - - +
49A VAL* 4.3 11.4 - - + -
188A VAL* 5.0 9.9 - - + -
192A GLN* 3.4 40.1 + - + +
193A MET* 3.9 28.5 - - + -
196A CYS* 4.2 20.5 - - - -
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Residues in contact with ARG 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 LEU 3.0 20.6 + - - +
41A ALA* 3.6 5.8 - - - +
43A VAL* 1.3 70.7 - - + +
45A GLY* 1.3 54.8 + - - +
113A ARG* 2.8 25.8 + - - -
192A GLN* 3.3 15.7 - - - +
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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