Contacts of the helix formed by residues 2 - 20 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I PHE* 1.3 84.6 - - - +
3I LEU* 1.3 62.7 + - - +
4I ILE* 3.2 13.3 - - - +
5I GLU* 3.0 30.4 + - - +
6I LEU* 3.4 14.6 + - - +
1J PHE* 3.6 14.8 - - + -
5J GLU* 3.6 7.4 - - - +
9J VAL* 3.9 2.4 - - - +
20L LEU* 3.4 45.5 + - + +
21L ILE* 3.9 11.9 - - + -
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Residues in contact with LEU 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 1.3 72.5 - - - +
4I ILE* 1.3 55.7 + - - +
6I LEU* 3.2 12.8 + - + +
7I LEU* 2.7 42.3 + - + +
5J GLU* 2.9 25.7 + - + +
8J ILE* 4.1 16.8 - - + -
9J VAL* 3.6 19.5 - - + -
12J ILE* 5.7 2.7 - - + -
22M PRO* 4.3 19.1 - - + -
23M ASN 5.2 1.8 - - - +
27M ALA* 4.4 25.8 - - + -
45P LYS* 4.0 29.1 - - + +
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Residues in contact with ILE 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I THR* 3.2 17.0 - - - +
3I LEU* 1.3 79.8 - - - +
5I GLU* 1.3 59.1 + - - +
7I LEU* 4.0 9.2 - - + -
8I ILE* 3.0 29.4 + - - +
21L ILE* 4.0 19.5 - - + -
22L PRO* 3.9 14.8 - - + -
24L LEU* 4.0 16.2 - - + -
41P ASN* 5.0 4.0 - - - +
44P VAL* 4.1 16.2 - - + +
45P LYS* 3.8 39.1 - - + +
48P GLU* 3.7 29.4 - - + -
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Residues in contact with GLU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE 4.3 0.2 - - - +
2A THR* 3.6 6.2 - - - -
3A LEU* 2.9 41.0 + - + +
1I PHE* 3.2 41.7 - - - -
2I THR* 3.0 23.7 + - - +
4I ILE* 1.3 76.0 - - - +
6I LEU* 1.3 58.6 + - - +
8I ILE* 3.5 10.8 - - - +
9I VAL* 3.1 19.2 - - - +
20L LEU 5.1 1.3 - - - +
22L PRO* 4.0 21.1 - - + -
41O ASN* 5.9 0.7 + - - -
45O LYS* 4.5 10.1 - - - +
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Residues in contact with LEU 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 4.1 14.1 - - + +
1I PHE* 3.9 20.6 - - + -
2I THR 3.4 11.1 + - - +
3I LEU* 3.2 15.5 + - + +
5I GLU* 1.3 78.8 - - - +
7I LEU* 1.3 58.5 + - - +
9I VAL* 3.3 6.5 + - + +
10I ILE* 3.0 36.5 + - + +
9J VAL* 3.8 29.6 - - + +
12J ILE* 3.5 35.4 - - + -
13J ILE* 4.2 10.8 - - + -
16J LEU* 4.3 19.1 - - + -
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Residues in contact with LEU 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I LEU* 2.7 25.6 + - + +
4I ILE* 3.4 10.5 + - + +
6I LEU* 1.3 71.6 - - - +
8I ILE* 1.3 59.4 + - - +
10I ILE* 3.4 12.3 + - + +
11I ALA* 3.0 24.6 + - - +
27M ALA* 5.6 8.5 - - + +
30M ARG* 4.3 20.6 - - + -
45P LYS* 3.4 47.3 - - + +
48P GLU* 4.6 7.4 - - + -
49P MET* 4.0 24.7 - - + -
52P ILE* 4.5 5.8 - - + +
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Residues in contact with ILE 8 (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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3A LEU* 4.1 19.7 - - + -
4I ILE* 3.0 17.0 + - - +
5I GLU* 3.5 18.6 - - - +
7I LEU* 1.3 74.7 - - - +
9I VAL* 1.3 63.8 + - - +
11I ALA* 3.2 5.9 + - - +
12I ILE* 3.0 34.9 + - + +
22L PRO* 5.2 0.7 - - + -
24L LEU* 3.4 49.1 - - + +
27L ALA* 4.2 11.2 - - + -
28L ARG* 3.7 17.7 - - + +
48P GLU* 3.5 22.9 - - + +
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Residues in contact with VAL 9 (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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1A PHE* 3.4 43.3 - - + +
2A THR 3.9 0.7 - - - +
3A LEU* 3.6 40.8 - - + +
6A LEU* 3.8 13.4 - - + +
5I GLU* 3.1 20.6 - - - +
6I LEU* 3.3 11.1 + - + +
7I LEU 3.3 0.2 - - - -
8I ILE* 1.3 73.9 - - - +
10I ILE* 1.3 64.0 + - - +
12I ILE 3.5 0.3 + - - -
13I ILE* 3.1 30.8 + - + +
16J LEU* 5.4 3.6 - - + -
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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 LEU* 3.0 27.3 + - + +
7I LEU* 3.6 15.3 - - + +
8I ILE 3.3 0.2 - - - -
9I VAL* 1.3 75.2 - - - +
11I ALA* 1.3 62.5 + - - +
13I ILE* 3.5 9.3 + - + +
14I ALA* 3.3 20.8 + - + +
12J ILE* 4.1 24.5 - - + -
16J LEU* 4.1 19.7 - - + -
27M ALA 5.3 3.4 - - - +
30M ARG* 3.5 24.2 - - + +
31M ALA* 4.6 12.1 - - + +
34M THR* 3.2 25.0 + - - +
52P ILE* 5.4 2.7 - - + -
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Residues in contact with ALA 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU 3.0 10.5 + - - +
8I ILE* 3.2 13.7 + - - +
10I ILE* 1.3 77.8 - - - +
12I ILE* 1.3 61.6 + - - +
14I ALA* 3.5 7.0 + - - +
15I ILE* 3.3 26.0 + - - +
28L ARG* 4.1 18.2 - - - +
48P GLU* 4.8 3.4 - - + +
52P ILE* 3.3 39.8 - - + +
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Residues in contact with ILE 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.7 3.4 - - + -
6A LEU* 3.5 30.7 - - + -
10A ILE* 4.1 5.8 - - + -
8I ILE* 3.0 25.3 + - + +
9I VAL 3.5 0.2 + - - -
11I ALA* 1.3 72.6 - - - +
13I ILE* 1.3 61.8 + - - +
15I ILE* 3.1 17.3 + - + +
16I LEU* 2.8 53.4 + - + +
27L ALA* 4.8 4.7 - - + +
28L ARG* 4.2 25.1 - - + +
31L ALA* 3.3 30.3 - - + -
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Residues in contact with ILE 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 4.0 15.9 - - + -
6A LEU* 4.2 14.6 - - + -
1H PHE 3.9 25.2 + - - +
9I VAL* 3.1 35.8 + - + +
10I ILE* 3.8 9.4 - - - +
11I ALA 3.4 0.2 - - - -
12I ILE* 1.3 74.8 - - - +
14I ALA* 1.3 57.9 + - - +
16I LEU* 4.1 5.3 - - - +
17I ALA* 2.9 33.5 + - + +
16J LEU* 4.9 5.6 - - + -
20J LEU* 4.0 20.4 - - + -
34M THR* 4.3 19.7 - - + -
37M THR* 6.1 3.1 - - + -
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Residues in contact with ALA 14 (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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10I ILE 3.3 10.6 + - - +
11I ALA* 3.6 10.5 - - - +
12I ILE 3.2 0.6 - - - -
13I ILE* 1.3 80.5 - - - +
15I ILE* 1.3 60.5 + - + +
17I ALA* 4.1 5.3 - - - +
18I ALA* 3.5 19.9 + - - +
37M THR* 5.6 6.7 - - - +
52P ILE* 4.9 14.8 - - + -
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Residues in contact with ILE 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ALA* 3.3 14.6 + - + +
12I ILE* 3.1 21.0 + - + +
14I ALA* 1.3 76.5 - - + +
16I LEU* 1.3 72.0 + - + +
18I ALA* 3.3 5.1 + - - +
19I VAL* 3.2 25.8 + - + +
28L ARG* 3.4 28.5 - - - +
31L ALA* 4.8 4.7 - - + +
32L ASN* 5.7 4.7 - - - +
35L VAL* 3.3 33.2 - - + -
51P GLN 6.1 0.4 - - - +
52P ILE* 6.5 1.6 - - - -
55P ASN* 5.7 7.6 - - - +
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Residues in contact with LEU 16 (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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6A LEU* 4.3 13.0 - - + -
9A VAL* 5.4 1.3 - - + -
10A ILE* 4.1 18.6 - - + -
13A ILE* 4.9 5.6 - - + -
1H PHE* 4.4 22.1 - - + -
12I ILE* 2.8 44.6 + - + +
13I ILE* 4.1 2.9 - - - +
15I ILE* 1.3 84.7 - - + +
17I ALA* 1.3 60.6 + - - +
19I VAL* 4.1 5.4 - - + -
20I LEU* 3.2 50.1 + - + +
21I ILE* 4.4 1.2 - - - +
31L ALA* 4.7 6.7 - - + +
34L THR* 4.4 22.0 - - + +
35L VAL* 5.6 0.2 - - + -
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Residues in contact with ALA 17 (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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1H PHE* 5.9 3.3 - - - +
13I ILE* 2.9 22.9 + - + +
14I ALA 4.1 4.0 - - - +
15I ILE 3.3 0.2 - - - -
16I LEU* 1.3 76.2 - - - +
18I ALA* 1.3 59.1 + - - +
21I ILE* 3.3 32.4 - - + +
37M THR* 4.0 26.9 - - + -
41M ASN* 5.8 7.8 - - + +
109M VAL* 4.7 10.9 + - + +
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Residues in contact with ALA 18 (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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14I ALA 3.5 11.2 + - - +
15I ILE* 3.3 10.0 + - - +
16I LEU 3.2 0.4 - - - -
17I ALA* 1.3 80.9 - - - +
19I VAL* 1.3 68.0 + - + +
21I ILE* 3.8 13.7 + - - +
70L LYS* 4.6 13.4 + - - -
107M LYS 5.6 0.3 - - - +
109M VAL 4.6 12.8 - - - +
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Residues in contact with VAL 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 3.2 19.2 + - + +
16I LEU* 4.0 4.7 - - + +
18I ALA* 1.3 80.4 - - + +
20I LEU* 1.3 81.7 + - + +
21I ILE 3.5 4.7 + - - +
34L THR* 4.4 3.6 - - + +
35L VAL* 4.0 40.4 - - + +
38L ALA* 3.9 23.1 - - + +
39L TYR 5.7 0.4 - - - +
42L ASP* 3.7 20.1 - - - +
70L LYS* 5.5 3.1 + - - +
73L PRO* 5.7 4.3 - - + -
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.0 21.3 - - + -
1G PHE 4.8 7.2 - - - +
2G THR* 3.3 26.6 + - + +
5G GLU* 5.1 1.4 - - - +
1H PHE* 3.4 34.3 - - + -
16I LEU* 3.2 34.1 + - + +
19I VAL* 1.3 78.4 - - + +
21I ILE* 1.3 62.2 - - - +
22I PRO* 3.3 8.5 - - - +
34L THR* 3.8 21.3 - - + -
38L ALA* 4.0 17.0 - - + -
42L 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