Contacts of the helix formed by residues 35 - 49 (chain I) in PDB entry 5BRR
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 SER 35 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PHE* 1.3 78.3 - - - +
36I PRO* 1.3 59.5 - - - +
37I TYR* 3.4 3.1 + - - +
38I GLY* 2.6 26.8 + - - -
39I VAL* 3.0 26.7 + - - +
169I LEU* 3.3 32.6 - - - +
322I GLN* 2.6 16.1 + - - -
324I VAL* 4.1 2.0 - - - -
371I LEU* 2.9 17.6 + - - +
372I PHE* 4.2 2.9 - - - -
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Residues in contact with PRO 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ALA 3.5 8.2 - - - +
13I SER* 3.6 22.4 - - - +
16I GLY* 3.6 13.0 - - - +
17I VAL* 4.4 1.1 - - + +
34I PHE* 3.4 12.8 - - + +
35I SER* 1.3 81.6 - - - +
37I TYR* 1.3 64.3 + - - +
39I VAL* 3.2 20.6 - - + +
40I ALA* 3.5 11.3 - - - +
370I VAL* 3.4 29.4 - - + +
371I LEU 3.7 6.5 - - - +
372I PHE* 4.0 4.5 - - - -
373I MET* 3.8 27.1 - - + -
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Residues in contact with TYR 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ALA* 5.4 7.6 - - + -
13I SER* 5.5 1.6 - - - +
35I SER* 3.2 4.2 + - - +
36I PRO* 1.3 75.1 - - - +
38I GLY* 1.3 61.4 + - - +
40I ALA* 2.9 7.3 + - + +
41I SER* 2.7 61.6 + - - -
75I LEU* 4.4 11.9 + - + +
78I LEU* 4.0 24.0 - - + -
79I TYR* 3.6 30.3 + - - +
82I LEU* 4.5 12.6 - - + -
93I THR* 4.1 23.5 - - + +
95I ASP* 5.2 2.5 + - - -
169I LEU* 4.6 6.5 - - + -
369I THR* 4.0 20.4 - - + -
370I VAL 3.2 16.4 + - - +
371I LEU* 4.0 21.5 - - + -
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Residues in contact with GLY 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I SER* 2.6 24.4 + - - -
37I TYR* 1.3 82.7 - - - +
39I VAL* 1.3 61.9 + - - +
41I SER* 3.3 9.2 + - - -
42I VAL* 3.5 7.1 + - - +
167I ASN* 3.1 39.5 + - - +
169I LEU* 4.2 3.1 - - - -
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 3.9 8.7 - - + -
16I GLY* 3.4 21.1 - - - -
19I VAL* 3.7 27.6 - - + -
34I PHE* 3.8 16.2 - - + -
35I SER 3.0 14.7 + - - +
36I PRO* 3.2 17.9 - - + +
38I GLY* 1.3 75.2 - - - +
40I ALA* 1.3 69.8 + - - +
42I VAL* 3.1 21.8 - - - +
43I LEU* 3.2 18.4 + - + +
167I ASN* 4.4 0.4 - - - -
286I LEU* 4.5 13.5 - - + -
290I LEU* 4.7 2.0 - - + -
322I GLN* 3.4 6.8 - - - +
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Residues in contact with ALA 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ALA* 3.5 35.4 - - + +
15I PHE* 3.8 20.0 - - + -
36I PRO 3.5 15.7 - - - +
37I TYR* 2.9 4.9 + - + +
39I VAL* 1.3 78.8 - - - +
41I SER* 1.3 59.5 + - - +
43I LEU 4.4 0.2 - - - +
44I ALA* 3.0 31.7 + - - +
62I MET* 3.4 7.1 - - + +
75I LEU* 5.3 1.0 - - - +
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Residues in contact with SER 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I TYR* 2.7 53.2 + - - -
38I GLY 3.8 4.7 - - - -
39I VAL 3.3 0.6 - - - -
40I ALA* 1.3 74.4 - - - +
42I VAL* 1.3 59.5 + - - +
44I ALA* 4.3 5.1 - - - +
45I MET* 3.2 24.4 + - - +
75I LEU* 4.8 15.1 - - - +
95I ASP* 3.8 19.2 + - - +
117I PHE* 5.5 0.2 - - - -
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Residues in contact with VAL 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I GLY 3.5 5.8 + - - +
39I VAL* 3.1 19.3 - - - +
41I SER* 1.3 79.9 - - - +
43I LEU* 1.3 72.1 + - + +
44I ALA 3.3 0.4 - - - -
45I MET* 3.2 9.7 + - + +
46I LEU* 2.8 29.5 + - - +
95I ASP* 3.1 38.6 - - + +
96I ALA 4.4 0.9 - - - +
165I LEU* 3.7 23.5 - - + +
166I VAL 3.8 12.1 - - - +
167I ASN* 3.9 14.4 - - + +
286I LEU* 5.4 5.4 - - + -
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 4.3 15.5 - - + -
39I VAL* 3.2 26.2 + - + +
40I ALA 3.4 1.5 + - - +
42I VAL* 1.3 86.4 - - + +
44I ALA* 1.3 55.7 + - - +
46I LEU* 3.2 5.1 + - + -
47I GLN 2.7 32.1 + - - -
58I ILE* 3.1 27.1 - - + +
62I MET* 3.7 18.8 - - + -
165I LEU* 4.4 12.8 - - + -
286I LEU* 5.1 2.7 - - + -
290I LEU* 4.4 16.8 - - + -
295I MET* 4.4 20.0 - - - -
298I MET* 4.4 18.6 - - + -
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Residues in contact with ALA 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I ALA 3.0 18.4 + - - +
41I SER 4.4 2.0 - - - +
43I LEU* 1.3 76.3 - - - +
45I MET* 1.3 61.9 + - - +
47I GLN* 2.9 23.2 - - - +
62I MET* 3.4 17.1 - - + +
64I PHE* 4.3 8.5 - - + -
66I ILE* 3.7 12.3 - - + +
75I LEU* 3.9 26.2 - - + -
117I PHE* 3.7 10.9 - - + -
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Residues in contact with MET 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I SER 3.2 18.4 + - - +
42I VAL* 3.2 11.7 + - + +
43I LEU 3.1 0.4 - - - -
44I ALA* 1.3 78.8 - - - +
46I LEU* 1.3 57.8 + - - +
47I GLN 3.0 0.2 - - - -
48I LEU* 2.8 30.8 + - - +
49I THR* 3.9 5.9 - - - +
95I ASP* 4.4 26.5 - - + +
96I ALA* 4.6 2.0 - - - +
97I ILE* 3.4 40.2 - - + +
113I PHE* 4.3 18.8 - - + -
117I PHE* 3.5 33.8 - - + -
119I SER* 5.2 8.7 - - - -
120I THR 5.9 2.0 - - - +
122I LYS* 5.9 1.3 - - - +
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Residues in contact with LEU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I VAL 2.8 20.0 + - - +
43I LEU* 3.7 6.7 - - + +
45I MET* 1.3 72.4 - - - +
47I GLN* 1.3 61.4 + - - +
48I LEU 3.2 0.4 - - - -
49I THR* 2.8 31.9 + - - +
50I THR* 3.2 24.4 + - + +
58I ILE* 3.7 21.1 - - + -
97I ILE* 4.2 17.6 - - + +
163I LEU* 5.6 1.1 - - + -
165I LEU* 3.7 26.9 - - + -
298I MET* 3.9 22.4 - - + -
306I PHE* 4.5 5.6 - - + -
317I VAL* 4.0 24.5 - - + -
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Residues in contact with GLN 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LEU 2.7 13.1 + - - +
44I ALA* 2.9 18.4 - - - +
45I MET 2.9 0.2 + - - -
46I LEU* 1.3 74.0 - - - +
48I LEU* 1.3 57.0 + - - +
50I THR* 2.7 16.6 + - - -
55I GLN* 3.2 15.6 - - + +
58I ILE* 3.3 16.7 - - + +
59I GLN* 3.3 33.3 + - + +
62I MET* 3.6 27.5 - - - +
64I PHE* 3.5 15.0 + - - -
65I LYS* 3.1 8.1 - - - -
66I ILE* 2.6 40.0 + - + +
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Residues in contact with LEU 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ALA 3.8 0.2 + - - -
45I MET 2.8 16.5 + - - +
47I GLN* 1.3 76.4 - - - +
49I THR* 1.3 60.6 + - + +
50I THR 3.2 5.6 + - - +
55I GLN* 4.5 2.9 - - - +
66I ILE* 3.9 16.8 - - + -
67I ASP* 4.6 8.1 - - - +
109I PHE* 3.6 16.6 - - + -
112I HIS* 4.1 21.5 - - + +
113I PHE* 3.6 42.8 - - + -
116I LEU* 3.2 30.3 - - + -
117I PHE* 4.1 9.2 - - + -
308I SER* 3.7 9.7 - - - -
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Residues in contact with THR 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I MET 3.9 13.7 - - - +
46I LEU* 2.8 26.4 + - - +
48I LEU* 1.3 79.6 - - - +
50I THR* 1.3 56.1 + - - +
97I ILE* 4.8 10.2 - - + +
109I PHE* 3.7 25.8 - - + -
113I PHE* 4.2 16.2 - - + -
121I VAL* 5.3 4.3 - - + -
163I LEU* 5.9 0.2 - - - +
306I PHE* 3.4 32.5 - - - +
308I SER* 4.4 5.6 - - - -
309I LEU* 3.9 18.7 - - + +
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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
------------------------------------------------------------
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