Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 1SIQ
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 LEU 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.7 34.3 + - + +
31A CYS* 3.1 23.0 + - + +
34A ARG* 1.3 74.9 - - - +
36A MET* 1.3 67.7 + - - +
37A PRO 3.2 2.5 - - - -
38A ARG* 3.0 39.5 + - - +
39A ILE* 3.2 9.9 + - - +
52A ILE* 4.0 22.2 - - + -
56A MET* 5.5 1.1 - - - -
86A LEU* 3.7 29.8 - - + -
89A VAL* 4.0 14.4 - - + -
93A TYR* 4.0 17.5 - - + -
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Residues in contact with MET 36 (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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31A CYS 3.0 7.4 + - - +
32A GLN* 3.5 35.9 - - - +
35A LEU* 1.3 73.0 - - - +
37A PRO* 1.3 70.9 - - + +
39A ILE* 3.0 28.5 - - - +
40A LEU* 4.4 1.4 + - - +
88A ARG 5.0 0.4 - - - +
89A VAL* 4.0 35.9 - - + +
263A PHE* 4.7 17.5 - - + -
355A HIS* 4.3 29.7 - - + +
358A ARG* 4.9 2.9 - - - -
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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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32A GLN 3.5 14.1 - - - +
33A GLU 3.2 21.1 - - - +
34A ARG* 3.7 10.5 - - - +
35A LEU 3.4 1.1 - - - -
36A MET* 1.3 95.9 - - + +
38A ARG* 1.3 59.0 + - + +
40A LEU* 5.0 4.3 + - - +
41A LEU 5.8 0.2 + - - -
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Residues in contact with ARG 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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34A ARG* 3.1 41.6 + - - +
35A LEU* 3.2 17.0 - - - +
37A PRO* 1.3 78.5 - - + +
39A ILE* 1.3 64.6 + - - +
40A LEU 3.4 1.9 + - - -
41A LEU* 3.8 5.2 + - - +
42A ALA* 3.1 22.7 + - - +
49A HIS* 4.2 27.0 - - + +
51A GLU* 4.9 13.1 + - - +
52A ILE* 3.7 26.4 - - - +
55A GLU* 3.1 38.4 + - - -
93A TYR* 3.8 15.7 - - - +
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Residues in contact with ILE 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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35A LEU 3.2 9.6 + - - +
36A MET* 3.0 36.8 - - - +
38A ARG* 1.3 75.4 - - - +
40A LEU* 1.3 69.7 + - - +
42A ALA* 4.0 1.8 - - - -
43A ASN* 2.9 26.1 + - + +
89A VAL* 4.5 3.1 - - + +
90A ASP* 3.5 33.7 - - + +
93A TYR* 4.0 13.5 - - + +
214A ALA* 3.8 20.6 - - + -
355A HIS* 4.3 7.9 - - + -
358A ARG* 3.7 36.1 - - - +
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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 MET 4.4 1.7 + - - +
37A PRO 5.0 3.6 + - - +
38A ARG 3.4 1.4 + - - -
39A ILE* 1.3 86.7 - - + +
41A LEU* 1.3 71.6 + - + +
43A ASN* 4.0 2.9 + - - +
44A ARG* 3.1 35.5 + - - +
352A ASP* 3.5 47.9 - - + +
353A GLU* 4.1 23.6 - - + +
355A HIS* 4.3 15.3 - - + +
358A ARG* 5.6 1.8 - - - +
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Residues in contact with LEU 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 5.8 0.2 + - - -
38A ARG 3.8 4.5 + - - +
40A LEU* 1.3 92.5 - - + +
42A ALA* 1.3 60.6 + - - +
44A ARG* 4.1 26.0 - - - +
45A ASN* 2.8 51.4 + - - +
47A VAL* 5.1 1.0 - - - +
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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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38A ARG 3.1 20.8 + - - +
39A ILE* 3.7 4.3 - - - +
41A LEU* 1.3 77.0 - - - +
43A ASN* 1.3 57.6 + - - +
46A GLU* 2.9 11.1 + - - -
47A VAL* 2.8 52.6 + - - +
49A HIS* 4.4 9.6 - - + -
93A TYR* 3.7 18.4 - - - +
214A ALA* 4.2 7.9 - - + -
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Residues in contact with ASN 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 ILE* 2.9 21.6 + - + +
40A LEU 4.0 2.0 + - - +
42A ALA* 1.3 77.3 - - - +
44A ARG* 1.3 63.1 + - - +
46A GLU 3.7 0.9 + - - -
90A ASP* 4.5 1.9 - - - +
213A ARG* 2.9 57.5 + - - +
214A ALA* 4.2 11.6 + - + +
352A ASP* 4.9 12.9 + - - +
358A ARG* 3.4 42.5 - - - +
361A MET* 5.5 6.4 - - - +
362A ASN* 4.4 6.1 + - - -
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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* 3.1 27.6 + - - +
41A LEU* 3.2 25.0 + - - +
43A ASN* 1.3 82.8 - - - +
45A ASN* 1.3 69.3 + - - +
213A ARG* 2.9 21.7 + - - +
352A ASP* 2.9 40.7 + - - +
353A GLU* 3.3 23.0 + - - -
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Residues in contact with ASN 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 LEU* 2.8 45.0 + - - +
44A ARG* 1.3 88.2 - - - +
46A GLU* 1.3 73.9 + - - +
47A VAL* 3.4 16.4 + - + +
213A ARG* 4.7 0.4 - - - +
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Residues in contact with GLU 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 ALA 2.9 6.5 + - - -
43A ASN 3.7 0.8 + - - -
44A ARG 3.5 1.6 - - - -
45A ASN* 1.3 80.1 - - - +
47A VAL* 1.3 58.3 + - - +
48A PHE 4.2 1.1 + - - -
205A ARG* 3.6 34.5 + - - +
206A ILE 4.7 0.7 - - - +
207A GLN* 5.7 0.5 - - - +
208A GLY* 4.6 10.0 + - - -
209A LYS* 4.2 27.4 + - - +
213A ARG* 3.2 66.2 + - + +
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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