Contacts of the helix formed by residues 8 - 27 (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 VAL 8 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ALA* 1.3 69.2 + - + +
10I HIS* 3.4 13.2 - - - +
11I LEU* 3.4 34.4 - - - +
12I ALA* 4.1 3.1 + - - +
64I PHE* 5.4 2.9 - - - -
71I MET* 5.3 17.7 - - + +
74I ALA* 3.5 31.6 - - + -
75I LEU* 5.7 5.8 - - + +
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Residues in contact with ALA 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 1.3 79.5 - - + +
10I HIS* 1.3 60.9 + - + +
11I LEU 3.2 1.3 - - - -
12I ALA* 3.5 8.8 + - - +
13I SER* 2.6 33.3 + - - -
74I ALA* 6.4 0.4 - - + -
75I LEU* 5.8 5.4 - - + -
78I LEU* 4.2 14.6 - - + -
367I THR* 4.4 14.4 - - - +
369I THR* 3.4 24.2 + - - +
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Residues in contact with HIS 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL 4.9 8.1 - - - +
9I ALA* 1.3 79.4 - - - +
11I LEU* 1.3 59.2 + - + +
13I SER* 4.1 1.6 - - - -
14I ASP* 2.8 42.0 + - - +
256I ALA* 3.3 39.5 - - + +
257I GLN* 4.2 16.0 + - - +
260I SER* 4.5 10.1 - - - -
367I THR 3.5 23.0 + - - -
368I GLY* 4.3 15.5 + - - -
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Residues in contact with LEU 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 3.4 25.9 + - - +
9I ALA 3.2 0.4 - - - -
10I HIS* 1.3 80.2 - - + +
12I ALA* 1.3 56.9 + - - +
14I ASP* 4.0 3.9 - - - +
15I PHE* 3.0 28.2 + - - +
18I ARG* 4.9 1.0 + - - -
62I MET 3.9 10.7 - - - +
63I GLY* 3.5 26.5 - - - +
64I PHE* 3.9 24.5 - - + -
71I MET* 5.5 4.9 - - + -
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL 4.1 2.3 + - - +
9I ALA* 3.5 13.0 + - - +
10I HIS 3.3 0.4 - - - -
11I LEU* 1.3 76.4 - - - +
13I SER* 1.3 61.8 + - - +
15I PHE* 3.4 5.9 + - - +
16I GLY 2.9 23.0 + - - -
36I PRO 3.5 1.7 - - - +
37I TYR* 5.7 7.4 - - + -
40I ALA* 3.5 28.5 - - + +
64I PHE* 4.5 17.9 - - + -
75I LEU* 5.1 12.3 - - + -
369I THR* 6.4 0.9 - - + -
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Residues in contact with SER 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ALA 2.6 21.9 + - - -
10I HIS* 3.7 3.8 - - - -
12I ALA* 1.3 77.3 - - - +
14I ASP* 1.3 52.9 + - - +
16I GLY* 3.0 4.0 + - - -
17I VAL* 2.7 39.0 + - - +
36I PRO* 3.6 12.4 - - - +
37I TYR* 5.5 0.9 - - - +
256I ALA* 4.3 5.2 - - - -
369I THR* 3.6 11.3 - - - +
370I VAL* 3.2 45.1 + - - -
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Residues in contact with ASP 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I HIS* 2.8 26.2 + - - +
11I LEU* 4.0 3.7 - - - +
13I SER* 1.3 73.5 - - - +
15I PHE* 1.3 65.2 + - - +
17I VAL* 3.2 8.0 + - - +
18I ARG* 3.1 38.9 + - - +
254I LEU 4.5 1.2 - - - +
255I SER* 3.1 18.5 - - - -
256I ALA* 2.9 35.5 + - - +
257I GLN 4.7 1.7 + - - -
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Residues in contact with PHE 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU 3.0 16.0 + - - +
12I ALA* 3.5 7.6 - - - +
13I SER 3.3 0.2 - - - -
14I ASP* 1.3 75.9 - - - +
16I GLY* 1.3 68.8 + - - +
18I ARG* 2.9 37.8 + - - +
19I VAL* 3.0 29.8 + - + +
39I VAL* 3.9 14.1 - - + -
40I ALA* 3.8 24.2 - - + -
43I LEU* 4.3 17.3 - - + -
61I ALA* 3.4 40.8 - - + -
62I MET* 3.8 26.9 - - + -
290I LEU* 4.4 7.9 - - + -
293I LEU* 4.0 15.3 - - + -
295I MET* 4.0 2.9 - - + -
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Residues in contact with GLY 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ALA 2.9 11.7 + - - -
13I SER 3.4 4.5 - - - -
15I PHE* 1.3 72.6 - - - +
17I VAL* 1.3 60.8 + - - +
19I VAL* 3.3 6.2 + - - +
20I PHE* 3.0 22.9 + - - +
34I PHE* 3.6 9.2 - - - -
36I PRO* 3.5 14.1 - - - +
39I VAL* 3.4 28.0 - - - -
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I SER 2.7 21.8 + - - +
14I ASP* 3.4 16.4 - - - +
15I PHE 3.1 0.2 - - - -
16I GLY* 1.3 72.9 - - - +
18I ARG* 1.3 57.2 + - + +
20I PHE* 2.6 29.8 + - - +
21I GLN* 2.8 27.5 + - + +
36I PRO* 4.5 4.7 - - + -
254I LEU* 3.4 30.1 - - + +
255I SER* 4.9 3.8 - - - +
370I VAL* 4.9 11.0 - - + -
373I MET* 3.7 33.0 - - + -
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Residues in contact with ARG 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU 4.9 0.8 + - - -
14I ASP* 3.1 40.1 + - - +
15I PHE* 2.9 24.7 + - - +
17I VAL* 1.3 76.7 - - - +
19I VAL* 1.3 62.4 + - - +
21I GLN* 3.2 32.2 + - - +
22I GLN* 3.2 22.1 + - - +
61I ALA 2.6 30.7 + - - -
62I MET 4.4 5.1 + - - -
293I LEU* 4.4 20.1 - - + +
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Residues in contact with VAL 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 3.0 47.0 + - + +
16I GLY* 3.4 10.8 - - - +
17I VAL 3.1 0.2 - - - -
18I ARG* 1.3 77.8 - - - +
20I PHE* 1.3 63.2 + - - +
22I GLN* 3.3 16.1 + - - +
23I VAL* 3.4 13.2 + - + +
34I PHE* 3.4 25.8 - - + -
39I VAL* 3.7 12.3 - - + -
286I LEU* 5.1 4.9 - - + -
289I PRO* 4.4 17.9 - - + -
290I LEU* 4.7 7.6 - - + -
293I LEU* 4.2 9.2 - - + +
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Residues in contact with PHE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLY 3.0 12.2 + - - +
17I VAL 2.6 14.2 + - - +
19I VAL* 1.3 68.5 - - - +
21I GLN* 1.3 54.5 + - - -
23I VAL* 3.2 4.8 + - + +
24I ALA* 2.7 50.5 + - + +
32I VAL* 3.9 22.0 - - + -
34I PHE* 3.4 34.7 - - + -
251I THR* 4.3 19.7 - - + -
254I LEU* 5.4 0.4 - - + -
359I LEU* 5.7 0.9 - - + -
373I MET* 3.4 40.4 - - + -
374I GLY* 3.7 40.2 - - - -
375I GLN* 4.1 12.6 - - + -
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Residues in contact with GLN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I VAL* 2.8 37.4 + - + +
18I ARG* 3.2 24.4 + - - +
20I PHE* 1.3 74.4 - - + +
22I GLN* 1.3 66.5 + - - +
24I ALA* 3.0 7.9 + - - +
25I GLN* 2.9 37.3 + - - +
251I THR* 3.9 15.9 + - - +
252I ASN* 3.5 40.6 + - + +
253I ILE* 5.0 0.4 - - - +
254I LEU 4.5 3.8 + - - -
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 3.2 20.4 + - - +
19I VAL* 3.4 8.7 - - - +
20I PHE 3.2 0.4 - - - -
21I GLN* 1.3 84.4 + - - +
23I VAL* 1.3 63.7 + - - +
25I GLN* 3.6 22.8 + - - +
26I ALA* 3.4 20.3 + - - +
289I PRO* 3.9 26.0 - - + +
292I ASN* 3.0 33.5 + - - +
293I LEU* 3.5 27.1 - - + +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I VAL 3.5 14.1 - - - +
20I PHE* 3.2 5.5 + - - +
22I GLN* 1.3 73.5 - - - +
24I ALA* 1.3 61.0 + - - +
26I ALA* 3.2 6.2 + - + +
27I SER* 2.8 34.0 + - - -
32I VAL* 4.2 21.1 - - + -
34I PHE* 4.4 15.3 - - + -
282I THR* 5.7 1.3 - - + -
284I VAL* 3.9 35.0 - - + -
289I PRO* 4.0 17.7 - - + -
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I PHE* 2.7 34.1 + - + +
21I GLN* 3.0 11.4 + - - +
23I VAL* 1.3 76.7 - - - +
25I GLN* 1.3 62.2 + - - +
27I SER* 3.1 25.5 + - - -
28I LYS 3.9 6.9 + - - +
32I VAL* 4.6 5.6 - - - +
248I SER* 5.7 3.1 - - - -
251I THR* 4.7 7.4 - - - +
375I GLN* 3.9 23.4 + - - +
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Residues in contact with GLN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I GLN* 2.9 16.1 + - - +
22I GLN* 3.6 32.9 + - - +
24I ALA* 1.3 76.5 - - - +
26I ALA* 1.3 64.6 + - + +
27I SER 3.3 0.2 - - - -
28I LYS* 4.0 6.6 + - - -
248I SER* 5.7 8.1 - - - +
292I ASN* 4.2 9.5 - - - +
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Residues in contact with ALA 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLN 3.4 13.4 + - - +
23I VAL* 3.2 8.6 + - + +
25I GLN* 1.3 82.5 - - + +
27I SER* 1.3 55.3 + - - +
28I LYS* 3.2 14.5 + - - +
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Residues in contact with SER 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I VAL* 2.8 17.4 + - - -
24I ALA 3.1 10.2 + - - -
26I ALA* 1.3 75.2 - - - +
28I LYS* 1.3 69.4 + - - +
30I ARG* 3.0 27.0 + - - +
31I ASN 5.8 0.2 - - - -
32I VAL* 2.8 35.1 - - - +
375I GLN* 4.0 2.1 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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