Contacts of the helix formed by residues 32 - 45 (chain M) in PDB entry 5XS0
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 THR 32 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203L ALA 4.4 0.9 + - - -
207L SER* 3.6 28.9 + - - +
30M GLN 3.4 5.6 + - - +
31M TYR* 1.3 76.1 - - - +
33M ALA* 1.3 57.6 + - - +
34M GLU* 3.8 16.9 + - - +
35M GLU* 3.2 27.7 + - - +
36M TYR* 2.7 34.6 + - - +
208V CYS* 4.5 1.1 - - - -
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Residues in contact with ALA 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M THR* 1.3 72.9 - - - +
34M GLU* 1.3 66.3 + - - +
36M TYR* 3.8 1.1 - - - +
37M GLN* 2.9 31.9 + - - +
205V TYR* 3.4 33.2 - - + +
208V CYS* 3.7 35.6 - - + +
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Residues in contact with GLU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L ALA* 3.4 28.8 - - + +
206L ASN* 4.6 16.2 - - - +
32M THR* 3.8 18.1 + - - +
33M ALA* 1.3 83.6 + - - +
35M GLU* 1.3 57.6 + - - +
37M GLN* 3.3 11.5 + - - +
38M ALA* 2.9 25.1 + - - +
205V TYR* 4.6 12.3 - - - +
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Residues in contact with GLU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200L VAL* 5.1 1.8 - - + +
203L ALA* 3.6 17.8 + - + +
204L ARG* 3.2 42.5 + - + +
207L SER* 3.8 17.5 + - - -
31M TYR* 3.4 30.9 - - + -
32M THR* 3.2 18.6 + - - +
34M GLU* 1.3 75.7 - - - +
36M TYR* 1.3 66.7 + - - +
38M ALA* 3.4 0.9 + - - +
39M ILE* 2.9 35.3 + - + +
79M PHE 4.8 0.7 - - - +
116M LYS* 3.3 21.3 + - - -
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Residues in contact with TYR 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L GLY* 4.7 1.3 - - - -
81L TYR* 3.4 29.6 - + - -
82L ASN* 3.9 15.5 - - - -
31M TYR* 4.2 12.4 - - + +
32M THR 2.7 23.8 + - - +
33M ALA* 3.8 5.2 - - - +
35M GLU* 1.3 73.7 - - - +
37M GLN* 1.3 63.2 + - + +
39M ILE* 3.9 0.5 - - - +
40M GLN* 2.9 47.0 + - + +
201V GLU* 3.2 24.4 + - - -
204V ARG* 2.3 56.1 + - + -
205V TYR* 4.7 11.2 - + - -
208V CYS* 4.1 19.5 - - - -
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Residues in contact with GLN 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ALA 2.9 18.6 + - - +
34M GLU* 3.8 9.7 + - - +
35M GLU 3.3 0.2 - - - -
36M TYR* 1.3 83.6 - - + +
38M ALA* 1.3 67.1 + - - +
40M GLN* 4.0 2.0 - - - +
41M LYS* 2.9 54.4 + - + +
201V GLU* 5.1 4.0 - - - +
205V TYR* 3.0 38.2 + - + -
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Residues in contact with ALA 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L SER* 3.9 16.8 + - - +
200L VAL* 3.6 33.8 - - + +
203L ALA* 3.9 4.5 - - + -
34M GLU 2.9 17.6 + - - +
35M GLU* 3.7 3.8 - - - +
36M TYR 3.3 0.2 - - - -
37M GLN* 1.3 81.4 - - - +
39M ILE* 1.3 58.0 + - - +
41M LYS* 3.9 4.1 - - - +
42M ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81L TYR* 3.4 31.2 - - + +
200L VAL* 3.8 13.2 - - + -
31M TYR* 3.6 36.3 - - + +
35M GLU* 2.9 29.8 + - + +
38M ALA* 1.3 74.6 - - - +
40M GLN* 1.3 57.8 + - - +
43M LEU* 2.9 38.4 + - + +
78M MET* 3.5 41.7 - - + +
79M PHE* 4.2 7.4 - - + -
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Residues in contact with GLN 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ASN* 3.1 30.3 + - - +
77L GLU* 4.6 7.8 + - - +
80L GLY* 3.3 5.9 - - - -
81L TYR* 3.8 22.1 + - + +
36M TYR* 2.9 38.3 + - + +
37M GLN* 4.0 3.4 - - - +
39M ILE* 1.3 79.5 - - - +
41M LYS* 1.3 64.6 + - + +
43M LEU* 3.6 9.6 + - - +
44M ARG* 3.8 27.7 + - - +
201V GLU* 3.9 13.5 + - - +
204V ARG* 3.2 23.0 - - - +
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Residues in contact with LYS 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M GLN* 2.9 47.7 + - + +
38M ALA* 3.9 3.8 - - - +
40M GLN* 1.3 78.0 - - + +
42M ALA* 1.3 61.9 + - - +
44M ARG* 3.3 42.5 + - - +
45M GLN* 4.1 6.0 + - - +
201V GLU* 5.5 12.4 + - - +
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Residues in contact with ALA 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L GLU* 3.4 32.5 - - - +
199L SER* 5.7 0.4 - - - +
200L VAL* 3.9 7.0 - - + -
38M ALA 2.9 18.4 + - - +
39M ILE 3.9 0.9 - - - +
41M LYS* 1.3 76.6 - - - +
43M LEU* 1.3 62.0 + - - +
45M GLN* 3.1 34.2 + - - +
78M MET* 3.8 14.3 - - - +
161M ALA* 3.5 8.1 - - - +
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Residues in contact with LEU 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L TYR* 3.6 26.0 - - + -
39M ILE* 2.9 35.0 + - + +
40M GLN* 4.0 7.4 - - - +
41M LYS 3.2 0.4 - - - -
42M ALA* 1.3 76.1 - - - +
44M ARG* 1.3 58.2 + - - +
45M GLN 3.2 0.2 - - - -
78M MET* 3.5 23.1 - - + -
79M PHE* 4.7 2.9 - - + -
158M PHE* 3.2 32.5 - - + +
159M GLY* 3.6 2.8 - - - -
160M ASN 2.9 27.2 + - - -
161M ALA* 3.0 20.6 + - + -
162M LEU* 4.2 22.9 - - + -
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Residues in contact with ARG 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73L ASN* 6.1 0.7 - - - +
77L GLU* 2.7 51.5 + - - +
40M GLN* 3.8 25.9 + - - +
41M LYS* 3.3 47.0 + - - +
42M ALA 3.2 1.0 - - - -
43M LEU* 1.3 77.5 - - - +
45M GLN* 1.3 65.7 + - + +
46M ARG* 3.3 8.1 + - - +
160M ASN* 3.2 24.1 + - - +
196V LEU* 3.6 21.8 - - - +
201V GLU* 4.7 9.9 + - - +
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Residues in contact with GLN 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L LYS 5.0 8.7 - - - +
192L LYS* 3.5 30.8 - - + +
197L GLU* 2.9 34.5 + - - +
41M LYS 4.3 4.4 + - - +
42M ALA* 3.1 26.3 + - - +
44M ARG* 1.3 76.5 - - - +
46M ARG* 1.3 60.3 + - - +
160M ASN* 3.4 0.7 - - - +
161M ALA* 3.0 30.5 + - + -
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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