Contacts of the helix formed by residues 15 - 29 (chain B) in PDB entry 1B6T
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 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.5 15.7 - - + +
14B ILE* 1.3 73.2 - - - +
16B ASN* 1.3 66.5 + - - +
17B GLY* 3.0 14.5 + - - -
18B HIS* 2.8 31.6 + - + +
19B ILE* 3.0 17.5 + - - +
127B ILE* 4.4 10.6 - - + +
128B SER* 4.5 3.9 - - - -
129B SER* 3.7 26.9 - - - +
132B VAL* 4.6 4.7 - - + -
145B PHE 3.8 10.1 - - - -
146B LEU* 3.8 15.7 - - + -
147B PRO* 4.2 2.0 - - - -
3000B COD 4.7 3.1 + - - -
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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
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15B THR* 1.3 73.1 - - - +
17B GLY* 1.3 57.8 + - - +
19B ILE* 3.6 10.9 - - - +
20B ASP* 2.9 27.9 + - - +
124B TRP* 3.4 36.6 + - + +
144B HIS 3.1 23.6 - - - +
145B PHE 2.9 20.8 + - - +
146B LEU 3.4 3.6 + - - +
147B PRO* 3.3 33.5 - - - +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 3.0 5.9 + - - -
16B ASN* 1.3 77.1 - - - +
18B HIS* 1.3 63.5 + - - +
20B ASP* 3.2 5.0 + - - +
21B ILE* 3.1 26.3 + - - +
124B TRP* 3.8 17.1 - - - +
127B ILE* 4.3 3.6 - - - +
3000B COD 3.5 31.8 + - - -
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Residues in contact with HIS 18 (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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7B TYR* 3.5 26.8 - - + -
11B PHE* 3.5 28.0 - + + -
13B PRO 3.8 4.3 - - - -
14B ILE* 3.5 17.3 - - + -
15B THR* 2.8 37.1 + - + +
17B GLY* 1.3 75.2 - - - +
19B ILE* 1.3 58.2 + - - +
21B ILE 3.2 1.0 + - - -
22B VAL* 2.9 28.3 + - - +
129B SER* 3.4 27.4 - - - -
3000B COD 3.4 48.6 + + - -
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.5 26.9 - - + -
15B THR 3.0 13.6 + - - +
16B ASN* 3.6 13.2 - - - +
17B GLY 3.2 0.2 - - - -
18B HIS* 1.3 75.1 - - - +
20B ASP* 1.3 60.6 + - - +
22B VAL* 3.4 5.6 - - + +
23B THR* 2.6 41.9 + - - +
58B ALA* 3.8 17.0 - - + +
59B THR* 3.7 20.9 - - + -
61B HIS* 4.9 14.4 - - + +
62B LEU* 5.1 1.3 - - + -
147B PRO* 4.0 16.8 - - + -
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Residues in contact with ASP 20 (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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16B ASN 2.9 15.1 + - - +
17B GLY* 3.3 10.5 - - - +
19B ILE* 1.3 78.8 - - - +
21B ILE* 1.3 64.1 + - - +
23B THR* 3.3 5.3 + - - -
24B ARG* 2.6 59.4 + - - +
120B PRO* 3.3 13.8 - - + +
121B SER* 3.1 33.5 + - - -
124B TRP* 3.7 12.7 + - + +
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Residues in contact with ILE 21 (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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7B TYR* 3.6 28.3 - - + +
17B GLY 3.1 13.9 + - - +
18B HIS 3.7 1.3 - - - +
20B ASP* 1.3 79.3 - - - +
22B VAL* 1.3 65.8 + - - +
24B ARG* 3.1 7.5 + - - +
25B ALA* 3.0 19.8 + - - +
87B ILE* 3.9 21.8 - - + -
89B GLY* 4.1 7.9 - - - -
118B LEU* 3.8 24.7 - - + +
119B MET 4.1 2.7 - - - -
120B PRO 3.7 20.0 - - - -
3000B COD 3.4 33.2 - - + +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.9 23.3 - - + -
18B HIS 2.9 15.7 + - - +
19B ILE* 3.4 17.0 - - - +
21B ILE* 1.3 76.8 - - - +
23B THR* 1.3 66.5 + - - +
25B ALA* 3.2 8.0 + - - +
26B THR* 3.1 26.4 + - - +
32B VAL* 3.9 21.5 - - + -
34B LEU* 4.1 15.5 - - + -
59B THR* 4.5 10.3 - - + -
62B LEU* 3.9 20.6 - - + -
65B VAL* 4.0 14.8 - - + -
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Residues in contact with THR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 2.6 29.6 + - - +
20B ASP* 3.5 6.7 - - - -
22B VAL* 1.3 78.4 - - - +
24B ARG* 1.3 63.0 + - + +
26B THR* 2.6 28.5 + - - +
27B GLN* 3.4 18.7 - - + +
61B HIS* 5.3 1.0 + - - -
62B LEU* 3.8 26.1 - - + +
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Residues in contact with ARG 24 (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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107A ARG* 3.4 32.8 - - - +
114A GLU* 3.1 42.2 + - - +
20B ASP* 2.6 48.4 + - - +
21B ILE* 3.6 10.8 - - - +
23B THR* 1.3 76.2 - - + +
25B ALA* 1.3 62.5 + - - +
27B GLN* 3.2 31.9 + - - +
28B MET* 3.7 12.8 + - - +
118B LEU* 4.0 14.1 - - + -
119B MET 3.4 13.5 + - - -
121B SER* 3.5 12.3 - - - +
503B SO4 4.0 4.9 + - - -
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 5.8 0.2 - - + -
21B ILE 3.0 13.2 + - - +
22B VAL* 3.3 14.8 - - - +
23B THR 3.1 0.2 - - - -
24B ARG* 1.3 77.6 - - - +
26B THR* 1.3 62.5 + - - +
27B GLN 3.2 0.5 + - - -
28B MET* 3.3 5.8 + - - -
29B PHE* 3.1 30.1 + - + +
32B VAL* 3.9 17.9 - - + -
87B ILE* 4.1 25.4 - - + -
118B LEU* 3.8 10.5 - - + +
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Residues in contact with THR 26 (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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22B VAL 3.1 13.9 + - - +
23B THR* 2.6 25.9 + - - +
25B ALA* 1.3 75.9 - - - +
27B GLN* 1.3 63.4 + - - +
29B PHE 3.3 18.9 - - - +
32B VAL* 4.0 12.3 - - + -
62B LEU* 4.8 10.0 - - + +
64B ASN* 4.1 24.8 - - + +
65B VAL* 3.4 29.8 - - + -
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Residues in contact with GLN 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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3A LYS* 2.8 18.1 + - - +
111A PRO 5.7 1.6 + - - -
112A GLU 5.9 1.4 + - - -
114A GLU* 3.7 26.3 + - - +
23B THR* 3.4 22.0 - - + +
24B ARG* 3.4 25.1 + - - +
25B ALA 3.1 1.0 - - - -
26B THR* 1.3 80.5 - - - +
28B MET* 1.3 59.8 + - + +
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Residues in contact with MET 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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3A LYS* 3.5 28.7 - - - +
28A MET 5.5 0.2 - - - +
29A PHE* 4.2 15.9 - - + -
85A VAL* 4.3 7.9 - - + -
114A GLU* 3.3 39.5 - - + -
116A VAL* 3.4 30.7 - - + -
3B LYS* 5.7 0.2 - - - +
24B ARG 3.9 11.0 - - - +
25B ALA* 3.3 5.1 + - - +
27B GLN* 1.3 81.0 - - + +
29B PHE* 1.3 100.3 + - + +
118B LEU* 4.1 10.8 - - + -
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Residues in contact with PHE 29 (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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28A MET* 4.2 15.5 - - + -
29A PHE* 4.0 24.5 - + - -
3B LYS* 3.9 25.6 - - + +
5B ALA* 4.0 24.9 - - + -
25B ALA* 3.1 21.2 + - - +
26B THR* 3.3 21.8 - - - +
27B GLN 3.7 0.4 - - - -
28B MET* 1.3 111.9 - - + +
30B ASP* 1.3 65.5 + - - +
31B HIS* 3.4 1.4 + - - +
32B VAL* 4.4 4.7 - - + +
64B ASN* 4.2 1.6 - - - +
85B VAL* 3.7 29.2 - - + -
87B ILE* 3.6 25.1 - - + -
116B VAL* 4.6 3.8 - - + -
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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