Contacts of the helix formed by residues 19 - 34 (chain B) in PDB entry 2HBF
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 ASN 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS 3.5 3.8 + - - -
18B VAL* 1.3 72.8 - - - +
20B VAL* 1.3 57.7 + - - +
21B ASP* 2.8 29.8 + - - +
22B GLU* 3.0 48.3 + - + +
23B VAL* 3.3 24.9 + - + +
117B HIS* 5.1 9.9 + - + +
118B PHE* 5.3 0.6 - - - -
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Residues in contact with VAL 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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15B TRP* 6.1 0.2 - - + -
18B VAL* 2.8 13.7 + - + +
19B ASN* 1.3 69.7 + - - +
21B ASP* 1.3 67.5 + - - +
22B GLU 3.6 0.2 - - - -
24B GLY* 5.5 0.7 - - - -
65B LYS* 3.8 28.6 + - + +
68B LEU* 3.5 40.6 - - + -
69B GLY* 5.2 2.9 - - - +
72B SER* 5.2 6.5 - - - +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 2.8 16.7 + - - +
20B VAL* 1.3 89.9 - - - +
22B GLU* 1.3 69.8 + - + +
24B GLY* 5.0 2.2 - - - -
25B GLY 5.0 1.7 + - - -
61B LYS* 4.7 15.9 - - - +
65B LYS* 4.1 24.4 + - - +
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Residues in contact with GLU 22 (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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19B ASN* 3.0 32.4 + - + +
20B VAL 3.6 0.2 - - - -
21B ASP* 1.3 90.7 - - + +
23B VAL* 1.3 56.1 + - + +
24B GLY 3.1 1.1 - - - -
25B GLY* 2.7 26.2 + - - -
26B GLU* 3.0 15.3 + - + +
61B LYS* 6.4 0.4 - - - -
117B HIS* 5.4 6.3 - - + +
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 5.9 0.2 - - + -
18B VAL* 4.2 20.4 - - + -
19B ASN* 3.3 22.6 + - + +
22B GLU* 1.3 72.9 - - - +
24B GLY* 1.3 59.2 + - - +
26B GLU* 3.0 9.9 + - - +
27B ALA* 2.9 29.8 + - - +
68B LEU* 4.4 5.4 - - + -
110B LEU* 4.2 19.5 - - + -
113B VAL* 3.7 18.1 - - + +
114B LEU* 4.3 13.5 - - + -
117B HIS* 4.0 31.8 - - + +
118B PHE* 5.9 0.9 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL 6.1 0.2 - - - -
21B ASP 5.0 1.5 - - - -
22B GLU 3.1 2.2 - - - +
23B VAL* 1.3 78.6 - - - +
25B GLY* 1.3 56.3 + - - +
27B ALA* 4.0 5.3 + - - +
28B LEU* 3.9 10.6 + - - +
64B GLY* 2.7 43.5 - - - +
65B LYS* 4.5 1.3 - - - -
67B VAL* 5.2 1.4 - - - +
68B LEU* 3.6 24.8 - - - +
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Residues in contact with GLY 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 ASP 5.0 1.6 + - - -
22B GLU* 2.7 16.4 + - - +
24B GLY* 1.3 72.1 - - - +
26B GLU* 1.3 56.3 + - - -
27B ALA 3.3 0.4 - - - -
28B LEU 3.4 0.7 + - - -
29B GLY* 2.9 27.5 + - - -
55B MET* 5.2 0.9 - - - +
60B VAL* 3.8 8.4 - - - +
61B LYS* 3.9 30.1 + - - -
64B GLY* 4.0 4.2 - - - -
65B LYS 4.7 0.6 - - - +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO* 4.2 10.2 - - - +
22B GLU* 3.0 11.1 + - + +
23B VAL* 3.0 11.1 + - - +
25B GLY* 1.3 78.6 - - - +
27B ALA* 1.3 57.8 + - - +
29B GLY* 3.8 1.3 - - - +
30B ARG* 2.9 78.3 + - - +
55B MET* 4.4 11.2 - - - +
113B VAL* 4.1 18.8 - - + +
116B HIS* 4.6 6.8 + - - -
117B HIS* 5.1 10.0 - - + -
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Residues in contact with ALA 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 VAL 2.9 14.7 + - - +
24B GLY* 4.4 5.8 - - - +
26B GLU* 1.3 76.6 - - - +
28B LEU* 1.3 61.1 + - - +
30B ARG* 3.8 0.8 - - - -
31B LEU* 2.8 27.9 + - - +
67B VAL* 6.5 1.3 - - + -
106B LEU* 4.2 12.3 - - + +
109B VAL* 3.5 10.0 - - + +
110B LEU* 4.5 26.5 - - + -
113B VAL* 4.0 17.0 - - + +
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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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24B GLY 3.9 10.4 + - - +
25B GLY 3.4 6.9 + - - +
27B ALA* 1.3 74.1 - - - +
29B GLY* 1.3 68.8 + - - +
31B LEU* 3.0 8.7 + - + +
32B LEU* 3.0 43.3 + - + +
42B PHE* 4.7 6.3 - - + -
45B PHE* 4.2 7.6 - - + -
60B VAL* 3.5 31.6 - - + +
63B HIS* 3.8 26.9 - - + -
64B GLY* 3.8 4.9 - - - +
67B VAL* 5.2 1.1 - - + -
106B LEU* 4.9 3.8 - - - -
148B NPN 3.9 31.2 - - + -
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Residues in contact with GLY 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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25B GLY 2.9 18.2 + - - -
28B LEU* 1.3 77.9 - - - +
30B ARG* 1.3 56.3 + - - +
32B LEU* 3.3 1.1 + - - -
33B VAL* 3.0 31.0 + - - +
54B VAL* 3.4 23.0 - - - +
55B MET* 3.2 15.0 - - - -
60B VAL* 3.9 7.1 - - - +
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Residues in contact with ARG 30 (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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117A PHE* 3.1 43.6 + - - -
118A THR 3.4 1.8 + - - -
119A PRO* 3.6 21.6 - - + +
122A HIS* 3.0 49.6 + - + +
26B GLU* 2.9 66.8 + - - +
27B ALA* 3.9 3.4 - - - +
29B GLY* 1.3 71.9 - - - +
31B LEU* 1.3 59.6 + - - +
33B VAL* 4.4 2.5 - - - +
34B VAL* 2.8 37.2 + - + +
55B MET* 3.4 13.6 - - + +
109B VAL* 4.9 7.0 - - + -
113B VAL* 4.2 13.0 - - + +
116B HIS* 4.0 13.4 + - - +
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Residues in contact with LEU 31 (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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27B ALA 2.8 18.6 + - - +
28B LEU* 3.0 14.8 + - + +
30B ARG* 1.3 69.3 - - - +
32B LEU* 1.3 56.2 + - + +
35B TYR* 2.8 60.1 + - + +
38B THR* 3.9 27.4 - - + +
102B ASN 4.6 2.7 - - - +
105B LEU* 4.2 5.4 - - + -
106B LEU* 3.8 32.8 - - + +
109B VAL* 4.3 7.0 - - + +
147B HEM 4.5 9.4 - - + -
148B NPN 3.8 35.4 - - + -
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Residues in contact with LEU 32 (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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28B LEU* 3.0 27.9 + - + +
29B GLY* 3.6 4.9 - - - +
31B LEU* 1.3 74.6 - - + +
33B VAL* 1.3 62.7 + - - +
36B PRO* 3.3 14.0 - - - +
38B THR* 3.6 17.5 - - - +
39B GLN* 3.2 35.1 + - + +
42B PHE* 3.5 37.9 - - + -
45B PHE* 5.3 0.9 - - + -
48B LEU* 3.8 24.7 - - + -
54B VAL* 3.8 24.0 - - + -
60B VAL* 4.2 12.3 - - + -
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Residues in contact with VAL 33 (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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119A PRO* 4.0 21.1 - - + +
120A ALA* 4.9 0.2 - - - -
123A ALA* 4.1 13.7 - - + +
29B GLY 3.0 20.8 + - - +
30B ARG* 3.3 4.0 + - - +
32B LEU* 1.3 78.8 - - - +
34B VAL* 1.3 62.9 + - + +
36B PRO* 3.7 13.0 - - - +
39B GLN* 4.7 4.2 + - - +
51B PRO* 3.9 39.5 - - + -
54B VAL* 4.0 12.1 - - + -
55B MET* 3.3 21.3 - - + -
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Residues in contact with VAL 34 (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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119A PRO 4.3 4.3 - - - +
122A HIS* 3.9 30.3 - - + +
123A ALA* 3.8 27.7 - - + +
126A ASP* 3.8 26.3 - - + +
127A LYS* 6.0 1.7 - - - +
30B ARG* 2.8 25.3 + - + +
33B VAL* 1.3 76.8 - - + +
35B TYR* 1.3 95.0 + - + +
36B PRO* 3.2 8.2 - - - +
37B TRP* 5.1 1.0 - - - -
109B VAL* 5.3 0.4 - - + -
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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