Contacts of the helix formed by residues 12 - 31 (chain B) in PDB entry 2BTO
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 GLY 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 1.3 75.3 - - - +
13B GLN* 1.3 68.0 + - - +
14B ALA 3.6 0.9 - - - -
16B ASN* 2.9 25.7 + - - +
71B VAL 3.0 12.3 + - - -
72B ASP* 3.5 20.4 - - - -
147B THR* 4.2 5.3 - - - +
1433B GTP 3.0 17.7 - - - -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 1.3 72.1 - - - +
14B ALA* 1.3 65.7 + - - +
16B ASN* 3.3 0.5 + - - -
17B GLN* 2.9 57.3 + - - +
72B ASP* 3.6 4.1 + - - +
76B SER* 6.3 0.2 - - - -
77B VAL* 3.7 27.7 - - + +
1433B GTP 2.4 50.3 + - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 1.3 79.4 - - - +
15B GLY* 1.3 64.2 + - - +
17B GLN* 3.3 0.9 + - - +
18B ILE* 2.9 36.6 + - + +
142B ALA* 3.3 32.3 - - + +
173B VAL* 4.9 0.7 - - + -
1433B GTP 3.2 44.4 + - + +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER* 3.6 8.1 - - - -
11B ILE 3.6 11.6 + - - -
12B GLY 3.5 2.4 + - - -
13B GLN 3.3 0.4 - - - -
14B ALA* 1.3 79.2 - - - +
16B ASN* 1.3 50.5 + - - +
18B ILE* 3.4 5.7 + - - +
19B ALA* 2.7 34.7 + - - +
140B LEU* 3.5 31.3 - - - +
141B HIS* 4.0 4.6 - - - +
142B ALA 4.4 0.2 - - - +
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER* 2.9 38.7 + - - -
12B GLY 2.9 23.8 + - - +
15B GLY* 1.3 72.8 - - - +
17B GLN* 1.3 60.4 + - - +
19B ALA* 3.5 3.9 - - - +
20B ALA* 2.9 30.7 + - - +
70B MET* 3.4 26.1 - - - +
71B VAL 3.1 20.1 - - - +
72B ASP* 3.9 8.0 - - - +
77B VAL* 3.8 16.6 - - + +
78B ILE* 4.2 7.8 - - + +
81B VAL* 4.5 5.0 - - + +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 2.9 49.1 + - - +
14B ALA 3.9 2.5 - - - +
16B ASN* 1.3 73.1 - - - +
18B ILE* 1.3 65.5 + - - +
20B ALA* 3.5 6.8 + - - +
21B SER* 3.3 21.7 + - - -
77B VAL* 3.6 18.6 - - + +
80B ASN* 5.3 7.1 - - - +
81B VAL* 5.9 0.7 - - - -
226B VAL* 3.9 15.4 - - - +
227B ASP* 5.9 1.1 - - - -
230B ASN* 4.0 10.5 + - - +
1433B GTP 3.1 23.8 + - - +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 2.9 26.9 + - + +
15B GLY* 3.6 5.4 - - - +
17B GLN* 1.3 73.7 - - - +
19B ALA* 1.3 66.1 + - - +
21B SER* 3.1 7.4 + - - -
22B PHE* 2.8 21.7 + - - +
140B LEU* 4.3 10.1 - - + -
141B HIS 5.9 1.1 - - - +
173B VAL* 3.8 19.7 - - + -
230B ASN* 3.2 26.0 - - + +
233B ILE* 3.8 44.9 - - + -
234B THR* 4.8 5.8 - - - +
237B LEU* 4.0 16.4 - - + -
1433B GTP 4.3 5.2 - - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 5.3 0.7 - - + -
10B SER* 3.2 31.2 - - - +
15B GLY 2.7 18.2 + - - +
16B ASN* 3.2 6.0 + - - +
18B ILE* 1.3 72.4 - - - +
20B ALA* 1.3 57.4 - - - +
22B PHE* 3.1 3.9 + - - +
23B TRP* 2.9 43.1 + - + +
70B MET* 4.0 10.3 - - + -
140B LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN 2.9 16.9 + - - +
17B GLN* 3.8 7.4 - - - +
18B ILE 3.3 0.2 - - - -
19B ALA* 1.3 74.3 - - - +
21B SER* 1.3 56.1 + - - +
23B TRP* 4.0 3.3 - - - +
24B LYS* 3.1 31.8 + - - +
70B MET* 4.3 7.9 - - + +
81B VAL* 4.2 24.2 - - + -
84B THR* 5.6 3.6 - - - +
85B SER* 6.4 1.1 - - - -
89B PHE* 5.0 4.3 - - + -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN 3.3 10.3 + - - -
18B ILE* 3.1 8.2 + - - -
20B ALA* 1.3 75.1 - - - +
22B PHE* 1.3 64.6 + - - +
24B LYS* 3.5 10.9 + - - +
25B THR* 3.2 26.3 + - - -
230B ASN* 4.3 12.2 + - - +
231B LEU* 4.8 9.4 - - - +
234B THR* 2.9 27.7 + - - +
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Residues in contact with PHE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.3 15.0 - - + -
18B ILE 2.8 13.0 + - - +
19B ALA* 3.5 9.2 - - - +
21B SER* 1.3 76.7 - - - +
23B TRP* 1.3 93.8 + + - +
25B THR* 3.2 4.5 + - - -
26B VAL* 3.0 54.5 + - + +
52B PHE* 4.0 22.9 - + - -
138B ILE* 6.2 0.7 - - + -
140B LEU* 4.9 3.1 - - + -
234B THR* 3.9 14.7 - - + +
237B LEU* 3.7 40.6 - - + -
238B ALA* 4.3 4.7 - - + -
241B THR* 3.8 20.6 - - + -
245B ARG* 5.2 0.2 - - - -
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.9 25.7 - - + +
19B ALA* 2.9 39.1 + - + +
20B ALA 4.2 1.3 - - - +
22B PHE* 1.3 85.0 - + - +
24B LYS* 1.3 67.1 + - - +
26B VAL* 4.0 5.5 - - + +
27B CYS* 2.9 30.7 + - - -
52B PHE* 3.3 47.1 - + + -
53B PHE* 3.9 20.2 - + - -
66B PRO* 3.5 25.8 - - + -
67B ARG 3.8 12.3 - - - -
68B ALA* 3.5 27.8 - - + +
70B MET* 4.5 1.3 - - + +
88B LEU* 4.5 5.6 - - + -
89B PHE* 3.9 31.0 - + + -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 2.6 39.0 + - + +
84A THR* 4.6 4.9 - - + +
20B ALA 3.1 20.5 + - - +
21B SER* 3.9 9.0 - - - +
22B PHE 3.3 0.2 - - - -
23B TRP* 1.3 77.1 - - - +
25B THR* 1.3 64.6 + - - +
27B CYS* 3.4 3.5 + - - +
28B LEU* 3.0 37.8 + - + +
34B PRO* 4.2 21.5 - - + +
88B LEU* 5.6 1.3 - - - +
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 3.2 18.2 + - - -
22B PHE* 3.6 4.3 - - - -
23B TRP 3.2 0.2 - - - -
24B LYS* 1.3 79.4 - - - +
26B VAL* 1.3 56.4 + - - +
28B LEU* 3.1 13.8 + - - +
29B GLU* 2.9 45.1 + - - +
234B THR* 3.4 17.1 - - + +
235B GLU* 6.2 0.7 - - - -
238B ALA* 4.2 15.5 - - + -
364B ILE* 4.2 23.2 - - + +
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.0 49.6 + - + +
23B TRP* 4.0 13.2 - - + +
25B THR* 1.3 75.4 - - + +
27B CYS* 1.3 65.3 + - - +
29B GLU* 3.2 6.6 + - - +
30B HIS* 3.0 41.7 + - + +
52B PHE* 4.9 2.0 - - + -
53B PHE* 3.5 28.9 - - + -
238B ALA* 5.2 3.1 - - - -
245B ARG* 4.0 27.6 - - - +
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Residues in contact with CYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP 2.9 25.6 + - - +
24B LYS 3.5 5.2 - - - +
26B VAL* 1.3 74.7 - - - +
28B LEU* 1.3 58.0 + - - +
30B HIS* 3.2 2.0 + - - -
31B GLY 2.9 9.7 + - - -
32B ILE* 2.8 51.7 + - - +
34B PRO* 3.8 17.3 - - + -
53B PHE* 4.0 18.6 - - - -
66B PRO* 5.0 0.4 - - - -
88B LEU* 3.8 35.2 - - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.6 39.7 - - + +
84A THR* 3.8 27.4 - - + -
24B LYS* 3.0 34.8 + - + +
25B THR* 3.1 10.7 + - - +
27B CYS* 1.3 76.5 - - - +
29B GLU* 1.3 61.8 + - - +
31B GLY* 3.4 5.9 + - - +
32B ILE 4.6 1.3 - - - -
34B PRO* 4.4 11.2 - - + -
46B ARG* 3.3 14.4 + - - -
364B ILE* 4.0 29.4 - - + +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 2.9 22.8 + - + +
26B VAL* 3.2 9.4 + - - +
28B LEU* 1.3 78.1 - - - +
30B HIS* 1.3 55.7 + - - +
46B ARG* 2.7 27.3 + - - +
238B ALA* 3.5 15.6 - - - +
245B ARG* 2.8 36.5 + - - +
246B PHE* 3.4 13.1 - - + -
324B ARG* 2.8 39.5 + - - +
361B GLN* 4.4 5.9 + - - +
362B PRO 4.9 1.6 - - - +
363B GLY* 3.9 8.4 - - - -
364B ILE* 3.9 18.8 + - + -
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Residues in contact with HIS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B VAL* 3.0 38.5 + - + +
27B CYS 4.1 0.4 - - - +
29B GLU* 1.3 75.5 - - - +
31B GLY* 1.3 61.9 + - - +
32B ILE* 3.3 19.5 - - + -
45B PRO* 3.2 8.2 - - + +
46B ARG* 2.8 52.4 + - - +
48B ASN 4.2 0.7 - - - -
49B TRP* 4.0 16.6 - - + -
52B PHE* 5.8 0.6 - - - +
53B PHE* 4.1 9.3 - + - -
245B ARG* 3.1 63.2 + - + +
246B PHE* 3.9 9.7 - + - -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER* 6.0 1.9 - - - -
27B CYS 2.9 4.7 + - - -
28B LEU* 3.4 4.9 + - - -
29B GLU 3.3 4.0 - - - -
30B HIS* 1.3 78.8 - - - +
32B ILE* 1.3 60.8 + - - +
33B ASP 4.0 0.7 + - - -
39B THR* 3.5 20.8 - - - +
40B ALA 5.2 0.9 + - - -
43B VAL* 5.7 1.4 - - - +
45B PRO* 5.0 0.6 - - - +
46B ARG* 3.5 21.7 - - - +
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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
------------------------------------------------------------
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