Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 6XXD
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 2 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B PHE* 1.3 84.3 - - - +
3B LEU* 1.3 62.4 + - - +
4B ILE* 3.2 14.0 - - - +
5B GLU* 3.0 29.7 + - - +
6B LEU* 3.4 15.1 + - - +
1C PHE* 3.6 14.4 - - + -
5C GLU* 3.6 7.4 - - - -
9C VAL* 3.9 2.5 - - - +
20E LEU* 3.3 45.3 + - + +
21E ILE* 3.9 12.3 - - + -
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Residues in contact with LEU 3 (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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45A LYS* 4.0 30.0 - - + +
2B THR* 1.3 71.9 - - - +
4B ILE* 1.3 55.3 + - - +
6B LEU* 3.2 13.4 + - + +
7B LEU* 2.7 43.0 + - + +
5C GLU* 2.9 25.9 + - + +
8C ILE* 4.2 15.9 - - + -
9C VAL* 3.6 20.4 - - + -
12C ILE* 5.8 2.2 - - + -
22F PRO* 4.3 18.8 - - + -
23F ASN 5.1 2.0 - - - +
27F ALA* 4.4 25.4 - - + -
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Residues in contact with ILE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 5.0 3.8 - - - +
44A VAL* 4.0 15.7 - - + +
45A LYS* 3.8 38.0 - - + +
48A GLU* 3.7 30.5 - - + -
2B THR* 3.2 16.6 - - - +
3B LEU* 1.3 79.6 - - - +
5B GLU* 1.3 59.3 + - - +
7B LEU* 4.0 9.4 - - + -
8B ILE* 3.0 29.7 + - - +
21E ILE* 4.0 19.7 - - + -
22E PRO* 3.9 14.8 - - + -
24E LEU* 4.0 16.4 - - + -
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Residues in contact with GLU 5 (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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1B PHE* 3.2 48.7 - - - -
2B THR* 3.0 24.4 + - - +
3B LEU 3.3 0.2 - - - -
4B ILE* 1.3 76.2 - - - +
6B LEU* 1.3 59.6 + - - +
8B ILE* 3.4 12.5 - - + +
9B VAL* 3.1 30.9 - - + +
20E LEU 5.1 1.1 - - - +
22E PRO* 3.9 21.8 - - + -
41H ASN* 5.9 0.6 + - - -
45H LYS* 4.5 16.4 - - - +
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Residues in contact with LEU 6 (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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1B PHE* 3.9 22.9 - - + -
2B THR 3.4 10.8 + - - +
3B LEU* 3.2 14.7 + - + +
5B GLU* 1.3 78.1 - - - +
7B LEU* 1.3 58.9 + - - +
9B VAL* 3.3 11.7 + - + +
10B ILE* 3.0 36.6 + - + +
9C VAL* 3.9 29.4 - - + +
12C ILE* 3.5 35.7 - - + -
13C ILE* 4.3 10.3 - - + -
16C LEU* 4.3 21.5 - - + -
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Residues in contact with LEU 7 (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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45A LYS* 3.4 48.0 - - + +
48A GLU* 4.5 7.6 - - + -
49A MET* 4.0 24.5 - - + -
52A ILE* 4.5 5.3 - - + +
3B LEU* 2.7 26.5 + - + +
4B ILE* 3.4 11.0 + - + +
6B LEU* 1.3 72.0 - - - +
8B ILE* 1.3 59.6 + - - +
10B ILE* 3.4 12.0 + - + +
11B ALA* 3.0 25.2 + - - +
27F ALA* 5.6 7.9 - - + +
30F ARG* 4.3 21.3 - - + -
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU* 3.5 23.5 - - + +
4B ILE* 3.0 16.6 + - - +
5B GLU* 3.4 18.8 - - + +
7B LEU* 1.3 73.8 - - - +
9B VAL* 1.3 66.3 + - + +
11B ALA* 3.2 5.4 + - - +
12B ILE* 3.0 35.6 + - + +
22E PRO* 5.2 3.6 - - + -
24E LEU* 3.4 49.8 - - + +
27E ALA* 4.2 13.2 - - + -
28E ARG* 3.7 17.9 - - + +
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Residues in contact with VAL 9 (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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5B GLU* 3.1 29.6 - - + +
6B LEU* 3.3 15.8 + - + +
7B LEU 3.3 0.4 - - - -
8B ILE* 1.3 77.5 - - + +
10B ILE* 1.3 63.8 + - - +
12B ILE* 3.5 7.0 + - - +
13B ILE* 3.1 40.2 + - + +
16C LEU* 5.4 7.6 - - + -
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Residues in contact with ILE 10 (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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52A ILE* 5.4 3.1 - - + -
6B LEU* 3.0 27.1 + - + +
7B LEU* 3.6 15.9 - - + +
8B ILE 3.3 0.2 - - - -
9B VAL* 1.3 75.3 - - - +
11B ALA* 1.3 61.5 + - - +
13B ILE* 3.5 9.3 + - + +
14B ALA* 3.3 20.5 + - + +
12C ILE* 4.2 24.5 - - + -
16C LEU* 4.1 18.6 - - + -
27F ALA 5.3 3.4 - - - +
30F ARG* 3.5 24.2 - - + +
31F ALA* 4.6 12.3 - - + +
34F THR* 3.3 25.5 + - - +
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Residues in contact with ALA 11 (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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48A GLU* 4.8 3.1 - - + +
52A ILE* 3.2 39.9 - - + +
7B LEU 3.0 10.1 + - - +
8B ILE* 3.2 13.6 + - - +
10B ILE* 1.3 77.4 - - - +
12B ILE* 1.3 61.1 + - - +
14B ALA* 3.5 6.7 + - - +
15B ILE* 3.3 26.3 + - - +
28E ARG* 4.1 18.6 - - - +
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Residues in contact with ILE 12 (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 ILE* 3.0 26.1 + - + +
9B VAL* 3.5 6.9 + - - +
11B ALA* 1.3 72.4 - - - +
13B ILE* 1.3 60.7 + - + +
15B ILE* 3.1 17.5 + - + +
16B LEU* 2.8 55.1 + - + +
27E ALA* 4.8 5.4 - - + +
28E ARG* 4.2 25.4 - - + +
31E ALA* 3.2 30.3 - - + -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.1 37.1 + - + +
10B ILE* 3.8 9.4 - - - +
11B ALA 3.4 0.2 - - - -
12B ILE* 1.3 76.3 - - + +
14B ALA* 1.3 59.1 + - - +
16B LEU* 3.9 7.2 - - + +
17B ALA* 2.9 34.0 + - + +
16C LEU* 4.9 6.7 - - + -
20C LEU* 4.1 33.2 - - + -
34F THR* 4.3 19.7 - - + -
37F THR* 6.1 3.1 - - + -
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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
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52A ILE* 4.9 15.0 - - + -
10B ILE 3.3 10.5 + - - +
11B ALA* 3.6 11.7 - - - +
12B ILE 3.2 0.8 - - - -
13B ILE* 1.3 79.4 - - - +
15B ILE* 1.3 61.6 + - + +
17B ALA* 4.1 4.9 - - - +
18B ALA* 3.5 20.6 + - - +
37F THR* 5.6 6.1 - - - +
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Residues in contact with ILE 15 (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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51A GLN 6.1 0.4 - - - +
52A ILE* 6.5 2.2 - - + -
55A ASN* 5.7 7.6 - - - +
11B ALA 3.3 15.0 + - - +
12B ILE* 3.1 20.7 + - + +
14B ALA* 1.3 76.9 - - + +
16B LEU* 1.3 71.9 + - + +
18B ALA* 3.3 5.4 + - - +
19B VAL* 3.2 25.8 + - + +
28E ARG* 3.4 28.7 - - - +
31E ALA* 4.8 4.7 - - + +
32E ASN* 5.7 4.7 - - - +
35E VAL* 3.3 33.0 - - + -
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Residues in contact with LEU 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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12B ILE* 2.8 43.9 + - + +
13B ILE* 4.1 7.0 - - + +
15B ILE* 1.3 85.3 - - + +
17B ALA* 1.3 61.1 + - - +
19B VAL* 4.1 5.4 - - + -
20B LEU* 3.2 50.7 + - + +
21B ILE* 4.4 1.0 - - - +
31E ALA* 4.7 6.5 - - + +
34E THR* 4.4 26.0 - - + +
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Residues in contact with ALA 17 (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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13B ILE* 2.9 24.0 + - + +
14B ALA 4.1 4.3 - - - +
15B ILE 3.3 0.2 - - - -
16B LEU* 1.3 76.9 - - - +
18B ALA* 1.3 59.4 + - - +
21B ILE* 3.3 31.7 - - + +
37F THR* 4.0 26.9 - - + -
41F ASN* 5.8 7.6 - - + +
109F VAL* 4.7 10.7 + - + +
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Residues in contact with ALA 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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14B ALA 3.5 10.8 + - - +
15B ILE* 3.3 10.0 + - - +
16B LEU 3.2 0.4 - - - -
17B ALA* 1.3 81.3 - - - +
19B VAL* 1.3 68.7 + - + +
20B LEU 3.7 0.2 + - - -
21B ILE* 3.8 13.5 + - - +
70E LYS* 4.5 13.5 + - - -
107F LYS 5.6 0.3 - - - +
109F VAL 4.6 12.8 - - - +
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Residues in contact with VAL 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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15B ILE* 3.5 17.7 - - + +
16B LEU* 4.0 4.7 - - + +
18B ALA* 1.3 80.3 - - + +
20B LEU* 1.3 78.8 + - + +
21B ILE 3.5 4.7 + - - +
34E THR* 4.4 3.1 - - + +
35E VAL* 4.0 40.6 - - + +
38E ALA* 3.9 26.8 - - + +
39E TYR 5.7 0.4 - - - +
42E ASP* 3.7 20.1 - - - +
70E LYS* 5.5 3.2 + - - +
73E PRO* 5.7 4.0 - - + -
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Residues in contact with LEU 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 LEU* 3.2 43.1 + - + +
19B VAL* 1.3 79.7 - - + +
21B ILE* 1.3 67.4 + - + +
22B PRO* 3.3 10.2 - - - +
34E THR* 3.8 23.3 - - + -
38E ALA* 4.0 17.3 - - + -
42E ASP* 6.1 0.2 - - - -
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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
------------------------------------------------------------
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