Contacts of the helix formed by residues 2 - 20 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K PHE* 1.3 83.9 - - - +
3K LEU* 1.3 62.0 + - - +
4K ILE* 3.2 13.6 - - - +
5K GLU* 3.0 28.4 + - - +
6K LEU* 3.4 15.1 + - - +
1L PHE* 3.6 13.9 - - + -
5L GLU* 3.6 7.2 - - - -
9L VAL* 3.8 2.3 - - - +
20N LEU* 3.4 46.4 + - + +
21N ILE* 3.9 12.3 - - + -
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Residues in contact with LEU 3 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 1.3 71.9 - - - +
4K ILE* 1.3 55.0 - - - +
6K LEU* 3.2 13.6 + - + +
7K LEU* 2.7 45.5 + - + +
5L GLU* 2.9 27.1 + - + +
8L ILE* 4.1 15.9 - - + -
9L VAL* 3.6 20.6 - - + +
12L ILE* 5.7 2.9 - - + -
22O PRO* 4.3 25.8 - - + -
23O ASN 5.1 2.0 - - - +
27O ALA* 4.4 25.4 - - + -
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Residues in contact with ILE 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 3.2 17.3 - - - +
3K LEU* 1.3 78.7 - - - +
5K GLU* 1.3 58.2 + - - +
7K LEU* 4.0 23.8 - - + -
8K ILE* 3.0 30.7 + - + +
21N ILE* 4.0 20.0 - - + -
22N PRO* 3.9 15.5 - - + -
24N LEU* 4.0 32.3 - - + -
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Residues in contact with GLU 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 3.6 6.6 - - - -
3J LEU* 2.9 43.0 + - + -
1K PHE* 3.2 41.9 - - - -
2K THR* 3.0 24.6 + - - +
4K ILE* 1.3 77.2 - - - +
6K LEU* 1.3 59.1 + - - +
8K ILE* 3.5 10.2 - - - +
9K VAL* 3.1 19.6 - - - +
20N LEU 5.2 1.1 - - - +
22N PRO* 4.0 22.9 - - + -
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Residues in contact with LEU 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J PHE 4.1 14.1 - - - +
1K PHE* 3.9 18.6 - - + -
2K THR 3.4 11.4 + - - +
3K LEU* 3.2 14.6 + - + +
5K GLU* 1.3 79.4 - - - +
7K LEU* 1.3 58.8 + - - +
9K VAL* 3.3 6.6 + - + +
10K ILE* 3.0 36.6 + - + +
9L VAL* 3.8 29.6 - - + +
12L ILE* 3.5 36.6 - - + -
13L ILE* 4.2 10.1 - - + -
16L LEU* 4.3 20.0 - - + -
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Residues in contact with LEU 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 2.7 29.0 + - + +
4K ILE* 3.7 23.8 - - + +
6K LEU* 1.3 71.9 - - - +
8K ILE* 1.3 60.9 + - - +
10K ILE* 3.4 11.7 + - + +
11K ALA* 3.0 25.7 + - + +
27O ALA* 5.5 8.5 - - + +
30O ARG* 4.3 28.5 - - + -
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Residues in contact with ILE 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 4.2 20.2 - - + -
4K ILE* 3.0 19.1 + - + +
5K GLU* 3.5 17.3 - - - +
7K LEU* 1.3 72.5 - - - +
9K VAL* 1.3 62.7 + - - +
11K ALA* 3.2 6.0 + - - +
12K ILE* 3.0 34.4 + - + +
22N PRO* 5.3 0.7 - - + -
24N LEU* 3.4 50.9 - - + +
27N ALA* 4.2 9.9 - - + -
28N ARG* 3.7 30.3 - - + +
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Residues in contact with VAL 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J PHE* 3.4 44.4 - - + +
2J THR 4.0 0.7 - - - -
3J LEU* 3.6 40.2 - - + +
6J LEU* 3.8 13.8 - - + +
5K GLU* 3.1 21.3 - - - +
6K LEU* 3.3 10.5 + - + +
7K LEU 3.3 0.6 - - - -
8K ILE* 1.3 74.3 - - - +
10K ILE* 1.3 65.7 + - - +
12K ILE 3.5 0.5 + - - -
13K ILE* 3.1 28.5 + - + +
16L LEU* 5.4 3.8 - - + -
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Residues in contact with ILE 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LEU* 3.0 27.1 + - + +
7K LEU* 3.6 16.4 - - + +
8K ILE 3.3 0.4 - - - -
9K VAL* 1.3 76.0 - - - +
11K ALA* 1.3 61.2 + - - +
13K ILE* 3.5 9.3 + - + +
14K ALA* 3.3 21.3 + - - +
12L ILE* 4.1 24.7 - - + -
16L LEU* 4.1 18.6 - - + -
27O ALA 5.2 3.1 - - - +
30O ARG* 3.5 24.5 - - + +
31O ALA* 4.5 13.0 - - + +
34O THR* 3.2 25.3 + - - +
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Residues in contact with ALA 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K LEU* 3.0 13.5 + - + +
8K ILE* 3.2 13.6 + - - +
10K ILE* 1.3 78.0 - - - +
12K ILE* 1.3 59.2 + - - +
14K ALA* 3.5 8.9 + - - +
15K ILE* 3.3 26.6 + - + +
28N ARG* 4.2 20.0 - - - +
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Residues in contact with ILE 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 5.7 3.1 - - + -
6J LEU* 3.5 30.5 - - + -
10J ILE* 4.1 6.1 - - + -
8K ILE* 3.0 25.1 + - + +
10K ILE 3.4 0.2 - - - -
11K ALA* 1.3 73.1 - - - +
13K ILE* 1.3 59.8 + - - +
15K ILE* 3.1 17.3 + - + +
16K LEU* 2.8 53.5 + - + +
27N ALA* 4.8 4.5 - - + +
28N ARG* 4.2 24.9 - - + +
31N ALA* 3.3 31.0 - - + -
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Residues in contact with ILE 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I PHE 3.9 24.6 + - - +
1J PHE* 4.0 8.1 - - + -
6J LEU* 4.3 14.8 - - + -
9K VAL* 3.1 36.5 + - + +
10K ILE* 3.8 10.3 - - - +
12K ILE* 1.3 75.6 - - - +
14K ALA* 1.3 56.9 + - - +
16K LEU* 4.1 5.2 - - - +
17K ALA* 2.9 34.2 + - + +
16L LEU* 4.9 5.6 - - + -
20L LEU* 4.0 28.3 - - + -
34O THR* 4.3 20.4 - - + -
37O THR* 6.1 3.4 - - + -
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Residues in contact with ALA 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ILE* 3.3 11.0 + - + +
11K ALA* 3.6 11.4 - - - +
12K ILE 3.2 0.4 - - - -
13K ILE* 1.3 80.2 - - - +
15K ILE* 1.3 61.1 + - + +
17K ALA* 4.1 4.9 - - - +
18K ALA* 3.5 20.4 + - - +
37O THR* 5.5 7.0 - - - +
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Residues in contact with ILE 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ALA 3.3 15.0 + - - +
12K ILE* 3.1 20.7 + - + +
14K ALA* 1.3 76.3 - - + +
16K LEU* 1.3 71.9 + - + +
18K ALA* 3.3 5.3 + - - +
19K VAL* 3.2 26.3 + - + +
28N ARG* 3.4 28.7 - - - +
31N ALA* 4.8 5.2 - - + +
32N ASN* 5.7 4.3 - - - +
35N VAL* 3.3 33.2 - - + -
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Residues in contact with LEU 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I PHE* 4.4 22.1 - - + -
6J LEU* 4.3 14.4 - - + -
9J VAL* 5.4 1.3 - - + -
10J ILE* 4.1 18.6 - - + -
13J ILE* 4.9 5.6 - - + -
12K ILE* 2.8 43.7 + - + +
13K ILE* 4.1 3.4 - - - +
15K ILE* 1.3 83.5 - - + +
17K ALA* 1.3 61.7 + - - +
19K VAL* 4.1 5.8 - - + -
20K LEU* 3.2 49.8 + - + +
21K ILE* 4.4 0.9 - - - +
31N ALA* 4.7 6.7 - - + +
34N THR* 4.4 22.4 - - + +
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Residues in contact with ALA 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I PHE* 5.9 3.3 - - - +
13K ILE* 2.9 23.6 + - + +
14K ALA 4.1 4.3 - - - +
16K LEU* 1.3 76.8 - - - +
18K ALA* 1.3 59.8 + - - +
21K ILE* 3.3 30.9 - - + +
37O THR* 4.0 27.4 - - + -
41O ASN* 5.8 7.4 - - + +
109O VAL* 4.7 10.5 + - + +
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Residues in contact with ALA 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ALA 3.5 10.8 + - - +
15K ILE* 3.3 9.1 + - - +
16K LEU 3.2 0.4 - - - -
17K ALA* 1.3 81.2 - - - +
19K VAL* 1.3 68.4 + - + +
20K LEU 3.7 0.2 + - - -
21K ILE* 3.8 13.9 + - - +
70N LYS* 4.5 13.4 + - - -
107O LYS 5.6 0.5 - - - +
109O VAL 4.6 13.2 - - - +
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Residues in contact with VAL 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ILE* 3.2 19.0 + - + +
16K LEU* 4.0 4.7 - - + +
18K ALA* 1.3 80.5 - - + +
20K LEU* 1.3 81.5 + - + +
21K ILE 3.5 5.2 + - - +
34N THR* 4.4 2.9 - - + +
35N VAL* 4.0 40.6 - - + +
38N ALA* 3.9 22.5 - - + +
39N TYR* 5.7 0.7 - - + +
42N ASP* 3.7 19.4 - - - +
70N LYS* 5.5 3.0 + - - +
73N PRO* 5.8 4.0 - - + -
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Residues in contact with LEU 20 (chain K).
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 4.8 7.0 - - - +
2A THR* 3.4 27.2 + - + +
5A GLU* 5.1 0.9 - - - +
1I PHE* 3.4 34.8 - - + -
13J ILE* 4.1 21.8 - - + -
16K LEU* 3.2 34.7 + - + +
19K VAL* 1.3 78.6 - - + +
21K ILE* 1.3 62.6 + - - +
22K PRO* 3.3 8.9 - - - +
34N THR* 3.9 21.5 - - + -
38N ALA* 4.0 17.5 - - + -
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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