Contacts of the helix formed by residues 2 - 25 (chain I) in PDB entry 2AXT
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 GLU 2 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 1.3 76.2 - - - +
3I THR* 1.3 71.7 + - - +
4I LEU 3.0 1.1 - - - -
5I LYS* 2.9 30.5 + - - +
6I ILE* 2.9 26.3 + - + +
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Residues in contact with THR 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET 4.4 6.7 + - - -
2I GLU* 1.3 83.3 + - - +
4I LEU* 1.3 57.1 + - - +
6I ILE* 3.3 13.8 + - + +
7I THR* 3.0 37.1 + - - +
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Residues in contact with LEU 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.7 35.4 - - + -
97A TRP* 4.6 6.1 - - + +
563A CLA 4.4 8.3 - - + -
487C UNK 3.8 41.5 - - + -
1I MET* 3.8 23.7 - - + +
2I GLU 3.0 0.4 - - - -
3I THR* 1.3 78.4 - - - +
5I LYS* 1.3 62.0 + - - +
7I THR* 4.4 8.5 - - + -
8I VAL* 2.9 46.7 + - + +
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Residues in contact with LYS 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.6 41.4 - - + +
1I MET 3.7 3.4 + - - +
2I GLU* 2.9 26.0 + - - +
4I LEU* 1.3 78.8 - - - +
6I ILE* 1.3 69.5 + - + +
8I VAL* 3.4 2.1 + - - +
9I TYR* 3.1 44.5 + - + +
201I MGE 3.0 39.7 + - - +
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Residues in contact with ILE 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU* 2.9 27.6 + - + +
3I THR* 3.5 17.0 - - + +
5I LYS* 1.3 77.3 - - + +
7I THR* 1.3 70.0 + - - +
9I TYR* 2.9 18.9 + - - +
10I ILE* 2.9 32.6 + - + +
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Residues in contact with THR 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A CLA 5.5 7.0 - - + -
3I THR* 3.0 20.1 + - - +
4I LEU* 3.8 12.4 - - + -
6I ILE* 1.3 83.7 - - - +
8I VAL* 1.3 63.3 - - + +
10I ILE* 3.0 7.5 + - - +
11I VAL* 2.8 46.9 + - + +
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Residues in contact with VAL 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.7 31.0 - - + -
563A CLA 3.8 51.1 - - + +
4I LEU* 2.9 26.1 + - + +
5I LYS 3.7 3.8 - - - +
7I THR* 1.3 81.5 - - + +
9I TYR* 1.3 52.7 + - + +
11I VAL* 3.2 8.1 + - - +
12I VAL* 2.6 56.5 + - + +
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Residues in contact with TYR 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TRP* 3.9 11.1 - + - -
563A CLA 3.1 76.9 + - + +
5I LYS* 3.1 38.9 + - + +
6I ILE* 2.9 13.7 + - - +
8I VAL* 1.3 74.1 - - + +
10I ILE* 1.3 60.1 + - + +
12I VAL* 3.7 3.7 - - + +
13I THR* 2.7 41.5 + - - -
201I MGE 3.3 43.0 + - - -
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Residues in contact with ILE 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 2.9 34.0 + - + +
7I THR* 3.2 8.5 - - - +
9I TYR* 1.3 79.1 - - + +
11I VAL* 1.3 59.9 + - + +
13I THR* 3.1 5.4 + - - -
14I PHE* 2.9 29.2 + - + +
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Residues in contact with VAL 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A CLA 4.0 41.5 - - + -
7I THR* 2.8 36.2 + - + +
8I VAL* 3.4 10.8 - - - +
10I ILE* 1.3 75.9 - - + +
12I VAL* 1.3 63.3 + - - +
14I PHE* 3.5 5.6 + - - +
15I PHE* 2.8 48.9 + - + -
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Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A CLA 3.7 63.3 - - + +
495C CLA 3.7 29.4 - - + -
8I VAL* 2.6 39.3 + - + +
9I TYR* 3.9 5.8 - - - +
11I VAL* 1.3 72.6 - - - +
13I THR* 1.3 57.9 + - - +
15I PHE* 3.5 2.6 + - - +
16I VAL* 2.9 41.3 + - + +
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Residues in contact with THR 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A CLA 3.3 36.3 - - + +
9I TYR 2.7 28.1 + - - -
10I ILE* 3.5 6.2 - - - -
12I VAL* 1.3 71.7 - - - +
14I PHE* 1.3 66.5 + - - +
16I VAL* 3.2 7.5 + - + +
17I LEU* 2.8 52.3 + - + +
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Residues in contact with PHE 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 6.1 2.2 - + - -
566A BCR 4.1 19.5 - - + -
10I ILE* 2.9 14.4 + - + +
11I VAL* 3.6 10.3 - - - +
12I VAL 3.3 0.2 - - - -
13I THR* 1.3 77.5 - - - +
15I PHE* 1.3 90.9 + + - +
17I LEU* 3.3 13.2 + - + +
18I LEU* 3.1 62.6 + - + +
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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
----------------------------------------------------------
35A VAL* 3.3 30.9 - - + +
36A ILE* 4.8 4.6 - - + +
39A PRO* 3.4 25.1 - - + -
563A CLA 3.6 33.9 - - + -
566A BCR 3.5 38.4 - - + -
11I VAL* 2.8 41.9 + - + -
12I VAL 4.0 2.5 - - - +
13I THR 3.2 0.4 - - - -
14I PHE* 1.3 95.3 - + - +
16I VAL* 1.3 65.4 + - - +
18I LEU* 3.3 7.9 + - + +
19I PHE* 3.0 23.4 + - - +
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 5.4 1.6 - - + -
563A CLA 5.1 5.4 - - + -
495C CLA 3.8 46.2 - - + -
12I VAL* 2.9 35.7 + - + +
13I THR* 3.2 7.6 + - + +
15I PHE* 1.3 76.0 - - - +
17I LEU* 1.3 57.6 + - + +
19I PHE* 3.5 5.1 + - - +
20I VAL* 2.8 46.7 + - + +
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I THR* 2.8 44.1 + - + +
14I PHE* 3.4 12.3 - - + +
16I VAL* 1.3 74.9 - - + +
18I LEU* 1.3 72.7 + - + +
19I PHE 2.8 1.6 + - - -
20I VAL* 2.9 16.6 + - + +
21I PHE* 3.1 40.4 + - + -
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Residues in contact with LEU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.7 30.4 - - + -
17A PHE* 4.5 15.5 - - + -
32A TRP* 3.4 15.1 - - + -
35A VAL* 4.3 12.8 - - + -
566A BCR 4.1 21.5 - - + -
14I PHE* 3.1 52.0 + - + +
15I PHE* 3.3 8.5 + - + +
17I LEU* 1.3 79.2 - - + +
19I PHE* 1.3 58.0 + - - +
21I PHE* 4.0 1.8 - - + +
22I GLY 2.8 27.2 + - - -
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Residues in contact with PHE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.3 29.1 - - - +
33A PHE* 3.4 32.8 - + - -
35A VAL* 4.7 2.2 - - + +
36A ILE* 3.9 22.2 - - + -
495C CLA 4.2 43.5 - - + -
506C BCR 4.9 9.9 - - + -
15I PHE 3.0 12.4 + - - +
16I VAL 3.6 7.9 - - - +
17I LEU 2.8 4.6 + - - -
18I LEU* 1.3 76.7 - - - +
20I VAL* 1.3 73.9 - - + +
22I GLY* 3.5 0.9 + - - -
23I PHE* 3.1 57.1 + + - -
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Residues in contact with VAL 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C CLA 6.0 0.4 - - + -
496C CLA 4.0 21.8 - - + -
506C BCR 3.4 38.7 - - + +
16I VAL* 2.8 31.9 - - + +
17I LEU* 2.9 9.2 + - + +
19I PHE* 1.3 84.1 - - + +
21I PHE* 1.3 67.2 + - + +
23I PHE 3.4 0.3 + - - -
24I LEU* 3.1 27.1 + - + +
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Residues in contact with PHE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.5 26.2 - + + -
17I LEU* 3.1 47.8 + - + +
18I LEU* 4.6 0.9 - - + -
20I VAL* 1.3 75.1 - - + +
22I GLY* 1.3 59.9 + - - +
24I LEU* 2.6 46.7 + - + +
25I SER* 2.7 15.5 + - - +
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Residues in contact with GLY 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.8 2.1 - - - -
32A TRP* 2.9 58.5 + - - -
18I LEU 2.8 15.5 + - - -
20I VAL 3.5 0.2 - - - -
21I PHE* 1.3 72.0 - - - +
23I PHE* 1.3 58.6 + - - +
25I SER* 3.5 18.0 - - - -
27I ASP* 3.7 5.7 - - - +
30I ARG* 4.9 0.5 + - - -
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Residues in contact with PHE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.4 22.9 - + + -
33A PHE* 4.4 5.8 - + - -
131A TRP* 4.3 13.9 - + - -
132A GLU* 3.9 11.0 - - - -
262C ARG 5.0 0.9 - - - +
263C ALA* 5.2 3.8 - - - +
449C ARG* 5.0 0.4 - - - -
495C CLA 2.9 38.1 - - + -
506C BCR 3.6 26.2 - - + +
19I PHE* 3.1 55.6 + + - -
20I VAL 4.0 0.7 - - - +
21I PHE 2.7 1.6 + - - -
22I GLY* 1.3 73.4 - - - +
24I LEU* 1.3 68.1 + - - +
25I SER 3.0 2.1 + - - -
26I GLY* 3.4 0.7 + - - -
27I ASP* 2.9 55.9 + - + +
28I PRO* 4.9 1.2 - - - +
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Residues in contact with LEU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C TRP* 4.3 27.0 - - + +
262C ARG* 4.0 12.5 + - - +
263C ALA* 4.3 15.1 - - + +
496C CLA 3.7 24.2 - - + -
506C BCR 3.6 18.6 - - + -
20I VAL* 3.1 22.8 + - + +
21I PHE* 2.6 39.7 + - + +
23I PHE* 1.3 68.1 - - - +
25I SER* 1.3 49.6 + - - -
26I GLY* 2.5 21.3 + - - -
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TRP* 3.3 30.1 + - - -
18A CYS* 3.8 6.5 - - - -
21I PHE 2.7 15.5 + - - -
22I GLY 3.5 13.2 - - - -
23I PHE 3.0 1.4 - - - -
24I LEU* 1.3 71.4 - - - +
26I GLY* 1.3 65.0 + - - +
27I ASP 3.7 0.7 - - - -
30I ARG* 3.0 25.1 + - - -
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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) + - + + + + + -
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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