Contacts of the helix formed by residues 6 - 24 (chain K) in PDB entry 1XK4
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 SER 6 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I THR 3.4 25.6 - - - -
41I GLU* 2.7 34.0 + - - -
4K LYS 3.4 3.7 + - - -
5K MET* 1.3 75.9 - - - +
7K GLN* 1.3 64.8 + - - +
8K LEU 3.6 0.3 + - - -
9K GLU* 3.0 25.3 + - - +
10K ARG* 2.9 23.6 + - - +
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Residues in contact with GLN 7 (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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11I SER* 2.9 35.8 + - - +
14I ASP* 3.0 27.0 + - - +
15I VAL* 3.6 11.9 - - + -
18I LYS* 2.6 43.3 + - - +
41I GLU* 3.6 2.9 + - - +
6K SER* 1.3 73.8 - - - +
8K LEU* 1.3 57.3 + - - +
10K ARG* 3.3 31.1 + - - +
11K ASN* 3.0 33.4 + - - +
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Residues in contact with LEU 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 4.1 33.0 - - + -
15I VAL* 4.1 13.4 - - + +
37I LEU* 4.8 4.0 - - + -
41I GLU* 3.1 36.4 + - + +
71I PHE* 4.4 24.5 - - + -
75I VAL* 4.6 7.0 - - + -
78I MET* 3.6 35.9 - - + -
7K GLN* 1.3 73.2 - - - +
9K GLU* 1.3 61.9 + - - +
11K ASN* 3.2 5.3 + - - +
12K ILE* 2.9 38.2 + - + +
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Residues in contact with GLU 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLU 3.6 8.1 - - - +
42I SER 3.5 2.4 - - - -
43I PRO* 3.1 45.8 - - + +
78I MET* 5.0 2.9 - - + -
4K LYS 4.1 2.9 - - - +
5K MET* 3.5 23.7 - - + +
6K SER* 3.0 40.6 + - - +
8K LEU* 1.3 78.3 - - - +
10K ARG* 1.3 56.6 + - - +
12K ILE* 3.4 7.1 + - - +
13K GLU* 2.9 28.9 + - - +
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Residues in contact with ARG 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K MET* 3.2 47.6 + - + -
6K SER 2.9 16.1 + - - +
7K GLN* 3.4 36.8 + - - +
9K GLU* 1.3 73.6 - - - +
11K ASN* 1.3 66.9 + - - +
13K GLU* 3.3 10.5 + - - +
14K THR* 2.9 33.4 + - - +
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Residues in contact with ASN 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ALA* 3.5 25.7 - - + +
11I SER* 2.5 53.7 + - - -
12I ILE* 3.5 15.7 - - + +
15I VAL* 4.2 3.0 - - - +
7K GLN* 3.0 20.2 + - - +
8K LEU* 3.2 6.5 + - - +
10K ARG* 1.3 80.0 + - - +
12K ILE* 1.3 64.1 + - - +
14K THR* 3.3 4.7 + - - -
15K ILE* 3.2 27.0 + - - +
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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
----------------------------------------------------------
12I ILE* 5.4 0.9 - - + -
75I VAL* 4.4 13.5 - - + +
78I MET* 3.5 47.3 - - + +
79I GLY* 3.8 21.8 - - - +
82I ALA* 3.9 9.9 - - + -
8K LEU* 2.9 29.8 + - + +
9K GLU* 3.8 5.4 - - - +
11K ASN* 1.3 78.0 - - + +
13K GLU* 1.3 58.1 + - - +
15K ILE* 3.2 15.2 + - + +
16K ILE* 3.0 45.2 + - + +
76K PHE* 5.8 0.4 - - + -
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Residues in contact with GLU 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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5K MET* 3.2 35.3 - - - +
9K GLU 2.9 18.3 + - - +
10K ARG* 3.5 8.7 - - - +
12K ILE* 1.3 76.2 - - - +
14K THR* 1.3 57.0 + - - +
16K ILE* 3.3 9.1 + - + +
17K ASN* 2.8 51.3 + - - +
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Residues in contact with THR 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I GLU* 3.8 36.6 - - + +
5I LEU* 4.4 2.7 - - - -
8I ALA* 3.9 11.0 - - + +
10K ARG* 2.9 17.6 + - - +
11K ASN* 3.5 10.0 + - - -
13K GLU* 1.3 76.1 - - - +
15K ILE* 1.3 53.4 + - - +
17K ASN* 4.2 3.9 - - - +
18K THR* 2.6 44.7 + - - +
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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
----------------------------------------------------------
5I LEU* 4.1 21.1 - - + -
8I ALA* 4.8 3.1 - - + -
9I LEU* 3.7 24.7 - - + -
12I ILE* 3.9 16.6 - - + -
75I VAL* 5.7 1.8 - - + -
11K ASN 3.2 15.0 + - - +
12K ILE* 3.2 15.0 + - + +
14K THR* 1.3 74.1 - - - +
16K ILE* 1.3 67.2 + - - +
18K THR* 3.4 2.1 + - - -
19K PHE* 3.0 22.0 + - - +
76K PHE* 4.0 22.9 - - + -
79K PHE* 4.1 7.5 - - + -
80K ILE* 4.3 9.4 - - + -
83K MET* 3.8 28.7 - - + -
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Residues in contact with ILE 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLY 4.1 0.9 - - - +
82I ALA* 3.6 34.1 - - + +
83I HIS* 3.6 24.0 - - + +
86I SER* 3.8 23.6 - - - +
12K ILE* 3.0 21.9 + - + +
13K GLU* 3.7 9.0 - - - +
15K ILE* 1.3 76.6 - - - +
17K ASN* 1.3 69.6 + - - +
19K PHE* 3.4 4.0 + - - +
20K HIS* 2.9 29.5 + - + +
76K PHE* 3.7 27.1 - - + -
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Residues in contact with ASN 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I SER* 6.0 0.7 - - - -
13K GLU* 2.8 46.4 + - - +
14K THR* 4.2 3.5 - - - +
16K ILE* 1.3 81.9 - - - +
18K THR* 1.3 60.9 + - - +
20K HIS* 3.5 9.7 + - + +
21K GLN* 2.9 27.2 + - - +
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Residues in contact with THR 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I GLU* 6.1 0.2 - - - +
5I LEU* 4.0 29.0 + - + +
14K THR* 2.6 29.8 + - - +
15K ILE 3.7 3.8 - - - -
17K ASN* 1.3 73.2 - - - +
19K PHE* 1.3 65.1 + - - +
21K GLN* 3.2 13.3 + - + +
22K TYR* 3.2 22.4 - - + -
40K LEU* 4.2 9.6 - - + -
44K ASP* 3.8 30.5 - - + +
79K PHE* 6.0 1.1 - - + -
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Residues in contact with PHE 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I HIS* 4.7 4.3 - + - -
15K ILE 3.0 14.1 + - - +
16K ILE 3.5 8.3 - - - +
18K THR* 1.3 76.8 - - - +
20K HIS* 1.3 62.1 + - + +
22K TYR 3.3 0.9 + - - -
23K SER* 2.9 36.0 + - - -
30K ASP* 3.4 42.4 - - - -
31K THR* 4.0 4.3 - - - -
32K LEU* 3.6 29.0 - - + +
40K LEU* 4.2 10.2 - - - +
74K LEU 3.6 14.8 - - - -
76K PHE* 3.4 45.5 - + + -
79K PHE* 3.6 32.5 - + + -
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Residues in contact with HIS 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K ILE* 2.9 20.7 + - + +
17K ASN* 3.7 12.1 - - + +
19K PHE* 1.3 78.6 - - + +
21K GLN* 1.3 68.5 + - - +
22K TYR 3.0 1.2 + - - -
23K SER* 3.3 18.0 + - - -
24K VAL* 3.3 40.0 + - + +
29K PRO* 4.8 4.1 + - + -
30K ASP* 5.4 5.1 + - - -
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Residues in contact with GLN 21 (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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17K ASN 2.9 14.5 + - - +
18K THR* 3.2 13.6 + - - +
20K HIS* 1.3 78.6 - - - +
22K TYR* 1.3 75.5 + - + +
24K VAL* 3.9 7.1 - - - +
25K LYS* 3.4 35.2 - - - +
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Residues in contact with TYR 22 (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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18K THR* 3.2 24.9 - - + -
19K PHE 3.3 1.8 + - - +
20K HIS 3.0 0.2 - - - -
21K GLN* 1.3 91.5 - - + +
23K SER* 1.3 67.0 + - - +
24K VAL 3.1 3.6 + - - -
25K LYS* 3.1 28.7 + - + +
32K LEU* 3.7 17.0 - - + -
36K GLU* 3.2 25.4 - - + +
39K GLU* 3.6 45.1 - - + -
40K LEU* 3.7 24.0 - - + -
43K LYS* 3.8 21.4 - - - +
44K ASP* 2.7 32.2 + - - -
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Residues in contact with SER 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19K PHE* 2.9 28.6 + - - -
20K HIS* 3.3 12.0 + - - -
22K TYR* 1.3 76.8 - - - +
24K VAL* 1.3 62.3 + - - +
25K LYS 3.3 0.9 + - - -
26K LEU 3.4 3.1 - - - +
28K HIS 3.2 5.4 - - - +
29K PRO* 2.7 22.9 + - - +
30K ASP* 4.0 2.9 + - - -
31K THR 3.2 32.5 - - - -
32K LEU* 3.6 6.9 - - - +
36K GLU* 3.7 3.8 - - - -
3522K CA 2.5 22.2 - - - -
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K HIS* 3.3 40.8 + - + +
21K GLN* 3.9 9.2 - - - +
22K TYR 3.1 1.2 - - - -
23K SER* 1.3 78.9 + - - +
25K LYS* 1.3 67.2 + - + +
26K LEU* 3.2 4.6 + - - -
29K PRO* 3.7 28.3 - - + +
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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