Contacts of the helix formed by residues 20 - 38 (chain A) in PDB entry 1A8H
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 LEU 20 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 1.3 74.4 - - - +
21A GLY* 1.3 58.3 + - - +
23A ALA* 4.1 5.4 - - + -
24A TYR* 2.8 30.4 + - - +
290A LEU* 3.5 30.1 - - + -
298A MET* 3.4 30.3 - - + -
306A VAL* 3.8 19.7 + - + +
308A PRO* 3.7 31.0 - - + +
320A LEU* 5.6 1.3 - - + -
324A LEU* 4.3 18.4 - - + -
336A VAL* 3.6 28.9 - - + -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 5.4 0.3 - - - -
19A HIS* 3.0 16.5 - - - -
20A LEU* 1.3 78.7 - - - +
22A HIS* 1.3 64.4 + - - +
24A TYR* 4.1 4.3 - - - +
25A THR* 3.5 25.6 + - - -
290A LEU* 5.4 5.4 - - - -
298A MET* 4.7 3.9 - - - +
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.5 42.8 + + + +
13A TYR* 5.3 2.1 + - + +
16A ALA* 4.6 11.1 - - - +
17A GLU 4.7 0.7 - - - -
18A PRO* 4.0 2.9 - - + -
19A HIS* 2.9 50.5 + + - +
21A GLY* 1.3 76.3 - - - +
23A ALA* 1.3 64.3 + - - +
26A THR* 2.7 32.2 + - - -
78A PHE* 3.6 28.4 - + + -
82A TRP* 3.9 16.2 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS 2.9 11.5 + - - +
20A LEU* 3.5 14.6 - - + +
22A HIS* 1.3 78.9 - - - +
24A TYR* 1.3 58.0 + - - +
26A THR* 3.3 1.2 + - - -
27A VAL* 2.8 37.4 + - + +
82A TRP* 4.3 6.2 - - + -
85A LEU* 3.9 28.9 - - + -
308A PRO* 4.2 17.7 - - + -
309A PHE* 5.0 2.5 - - + -
324A LEU* 5.5 2.5 - - + -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 2.8 21.3 + - + +
21A GLY* 4.1 4.7 - - - +
23A ALA* 1.3 72.9 - - - +
25A THR* 1.3 71.2 + - - +
27A VAL* 3.1 7.8 + - + +
28A VAL* 2.9 42.7 + - + +
287A GLY* 5.1 6.5 - - - -
288A GLY 5.2 4.9 - - - -
290A LEU* 3.6 35.2 - - + -
324A LEU* 3.6 40.4 - - + +
325A LEU* 5.6 0.2 - - - -
328A ILE* 3.3 34.1 + - + +
330A TYR* 3.4 42.7 - + - +
400A PHE* 5.3 1.2 - - - -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 4.3 3.4 - - - -
10A PRO* 3.8 29.0 - - + +
12A TYR* 3.7 10.8 - - - +
21A GLY 3.5 14.6 + - - -
24A TYR* 1.3 87.1 - - - +
26A THR* 1.3 62.3 + - - +
28A VAL* 3.3 6.5 + - - +
29A ALA* 3.1 21.7 + - - +
256A LEU* 3.9 25.6 - - + +
257A ILE* 4.7 9.5 + - - +
258A GLY* 4.9 4.0 + - - -
287A GLY* 6.2 0.2 - - - -
330A TYR* 4.8 7.1 + - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 4.2 11.3 - - + +
12A TYR* 3.0 15.1 + - - -
22A HIS 2.7 22.8 + - - -
23A ALA 3.7 2.2 - - - -
25A THR* 1.3 74.4 - - - +
27A VAL* 1.3 61.0 + - - +
29A ALA* 3.3 1.7 + - - +
30A ASP* 2.9 27.4 + - - +
45A PHE* 4.0 7.5 - - + -
47A THR* 4.9 2.7 - - - +
82A TRP* 3.5 31.2 - - + +
87A ILE* 3.7 35.0 - - + -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 2.8 32.4 + - + +
24A TYR* 3.1 6.5 + - + +
26A THR* 1.3 73.5 - - - +
28A VAL* 1.3 58.3 + - + +
30A ASP* 3.3 7.5 + - - +
31A PHE* 2.9 27.0 + - - +
85A LEU* 4.0 26.0 - - + -
87A ILE* 4.4 10.5 - - + -
321A ARG* 4.2 34.9 + - + +
324A LEU* 5.0 13.0 - - + -
325A LEU* 4.2 20.9 - - + -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 2.9 53.4 + - + +
25A THR 3.7 5.4 - - - +
27A VAL* 1.3 78.1 - - + +
29A ALA* 1.3 56.6 + - - +
31A PHE* 3.5 2.4 + - - +
32A LEU* 3.0 28.7 + - + +
256A LEU* 4.0 14.6 - - + -
325A LEU* 4.1 20.2 - - + -
330A TYR* 4.1 14.4 - - + -
400A PHE* 3.3 33.0 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.0 10.8 - - + +
9A THR* 3.6 10.3 - - + -
25A THR 3.1 12.6 + - - +
26A THR 3.6 3.4 - - - +
27A VAL 3.2 0.2 - - - -
28A VAL* 1.3 73.4 - - - +
30A ASP* 1.3 60.8 + - - +
32A LEU* 3.2 5.6 + - - +
33A ALA* 2.8 31.4 + - - +
45A PHE* 3.5 27.6 - - + -
256A LEU* 3.5 22.4 - - + +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR 2.9 17.5 + - - +
27A VAL* 3.5 5.8 - - - +
29A ALA* 1.3 76.7 - - - +
31A PHE* 1.3 56.6 + - - +
33A ALA* 3.2 1.4 + - - +
34A ARG* 2.8 46.9 + - - +
37A ARG* 5.1 0.2 + - - -
45A PHE* 3.6 15.7 - - + -
86A GLY 3.2 5.2 - - - +
87A ILE* 3.4 16.2 - - + -
88A ALA* 2.7 33.1 + - - +
321A ARG* 2.8 33.2 + - - +
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL 2.9 17.5 + - - +
28A VAL 3.7 3.6 - - - +
29A ALA 3.3 0.2 - - - -
30A ASP* 1.3 76.6 + - - +
32A LEU* 1.3 65.3 + - - +
35A TRP* 3.0 45.8 + + + +
321A ARG* 4.5 0.8 - - - +
325A LEU* 4.0 22.2 - - + -
395A VAL* 4.0 22.0 - - + -
400A PHE* 3.5 44.0 - + + -
403A ALA* 5.5 2.5 - - + -
404A LEU* 4.6 16.6 - - + -
451A LEU 5.2 1.3 - - - -
454A PRO* 3.4 46.8 - - + +
455A ALA* 3.6 16.2 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.8 16.6 - - + -
7A VAL* 4.4 3.6 - - + -
28A VAL 3.0 20.1 + - - +
29A ALA* 3.2 5.4 + - - +
31A PHE* 1.3 78.7 - - - +
33A ALA* 1.3 61.1 + - - +
35A TRP* 3.7 2.8 - - - +
36A HIS* 2.8 37.7 + - + -
254A TRP* 3.9 31.4 - - + -
256A LEU* 4.0 31.9 - - + -
395A VAL* 4.1 17.3 - - + +
398A LEU* 4.6 2.2 - - + -
400A PHE* 3.9 32.8 - - + -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.2 10.5 - - + -
7A VAL* 4.3 4.0 - - + -
29A ALA 2.8 16.2 + - - +
30A ASP 3.6 3.6 - - - +
32A LEU* 1.3 74.5 - - - +
34A ARG* 1.3 58.5 + - - +
36A HIS* 3.1 3.1 + - - +
37A ARG* 2.8 48.3 + - - +
43A THR* 4.2 6.1 + - - +
45A PHE* 3.7 32.1 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 2.8 47.1 + - - +
31A PHE 3.9 0.4 - - - +
33A ALA* 1.3 71.4 - - - +
35A TRP* 1.3 57.1 + - - +
37A ARG* 3.3 20.3 + - - +
38A LEU* 3.0 32.6 + - - +
86A GLY 2.9 28.7 + - - -
88A ALA* 3.5 23.0 - - - +
453A THR* 5.0 4.8 + - + +
454A PRO* 3.8 26.2 - - + +
457A PRO* 3.3 39.2 - - - +
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Residues in contact with TRP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.0 31.7 + + + +
32A LEU* 3.7 5.8 - - - +
34A ARG* 1.3 77.7 - - - +
36A HIS* 1.3 79.6 + + - +
38A LEU* 3.1 6.7 + - - +
39A ASP* 2.9 29.6 + - + +
388A ALA 4.6 1.6 - - - -
391A LEU* 3.7 29.4 - - + -
392A ARG* 3.9 30.2 + - + +
395A VAL* 3.8 36.1 - - + +
396A ARG* 5.7 1.4 - - - +
451A LEU* 3.8 21.8 - - + -
454A PRO* 3.7 29.1 - - + +
475A LEU* 3.9 36.4 - - + +
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Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.6 34.5 - + + -
32A LEU* 2.8 35.8 + - + +
33A ALA 3.1 4.5 + - - +
35A TRP* 1.3 92.2 + + - +
37A ARG* 1.3 63.9 + - - +
38A LEU 3.0 1.6 - - - -
39A ASP* 3.0 7.0 + - - +
40A GLY 3.4 0.2 + - - -
41A TYR* 2.9 66.9 + + + +
43A THR* 4.2 1.1 - - + -
254A TRP* 5.2 0.2 - + - -
395A VAL* 4.8 1.3 - - + -
396A ARG* 2.6 50.1 + - - -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 5.1 0.2 + - - -
33A ALA* 2.8 21.7 + - - +
34A ARG* 3.5 21.2 - - - +
36A HIS* 1.3 76.0 - - - +
38A LEU* 1.3 62.4 + - + +
40A GLY* 3.3 12.6 + - - -
41A TYR 4.0 4.6 + - - +
43A THR* 3.5 29.3 + - + +
45A PHE* 3.5 14.1 - - - +
88A ALA* 2.8 44.0 + - - +
90A ASP* 2.9 34.8 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.0 12.5 + - + +
35A TRP* 3.2 11.2 - - - +
36A HIS 3.0 0.2 - - - -
37A ARG* 1.3 75.9 - - + +
39A ASP* 1.3 55.5 + - - +
40A GLY 3.1 8.3 + - - -
450A ILE* 3.8 28.0 - - + +
453A THR* 4.2 17.3 - - + -
454A PRO* 4.0 21.5 - - + -
473A VAL* 3.7 23.3 - - + +
474A ARG* 4.0 9.7 - - - +
475A LEU* 3.1 49.6 + - + +
476A GLU* 4.7 0.9 + - - +
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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