Contacts of the helix formed by residues 3 - 19 (chain K) in PDB entry 4B86
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 PRO 3 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET 3.9 0.4 - - - +
2K ASN* 1.4 85.9 - - - +
4K VAL* 1.3 55.4 + - - +
5K ASN 3.4 2.2 - - - -
6K ALA* 4.3 9.4 - - + -
7K THR* 2.7 32.1 + - - +
63K GLN* 4.3 0.2 - - - +
65K TYR* 3.4 26.2 - - + +
93K ASN* 3.6 20.6 - - - +
95K GLN* 3.7 25.8 - - + +
96K LEU* 3.8 22.2 - - + +
99K LEU* 3.9 13.0 - - + -
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Residues in contact with VAL 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J GLN* 3.6 11.2 - - + +
241J GLN* 3.4 34.8 - - + +
2K ASN* 2.8 28.2 + - + +
3K PRO* 1.3 71.1 - - - +
5K ASN* 1.3 62.2 + - - +
7K THR* 3.0 6.0 + - - -
8K ALA* 2.9 36.1 + - + +
63K GLN* 3.6 17.6 + - - +
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Residues in contact with ASN 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K VAL* 1.3 76.9 - - - +
6K ALA* 1.3 61.4 + - - +
8K ALA* 3.3 5.0 + - - +
9K LEU* 2.9 41.9 + - + +
41K SER* 4.6 11.4 - - - -
63K GLN* 3.1 34.7 + - + +
65K TYR* 6.3 1.6 - - + -
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Residues in contact with ALA 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K PRO* 3.8 13.2 + - + +
4K VAL 3.5 0.2 - - - -
5K ASN* 1.3 77.7 - - - +
7K THR* 1.3 57.1 + - - +
9K LEU 3.9 0.2 - - - -
10K TYR* 2.9 30.0 + - - +
38K PHE* 3.8 5.4 - - - -
41K SER* 3.7 22.3 - - - +
42K LEU* 3.8 24.9 - - + -
63K GLN* 4.7 0.4 + - - -
65K TYR* 5.3 2.1 + - + -
96K LEU* 4.8 1.3 - - + -
99K LEU* 3.7 22.5 - - + +
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Residues in contact with THR 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I LEU* 4.6 9.0 - - + -
236I GLN* 4.4 8.7 - - - +
233J ILE* 5.0 2.0 - - + -
237J GLN* 2.9 31.3 + - - +
3K PRO 2.7 20.5 + - - +
4K VAL 3.0 7.3 + - - -
6K ALA* 1.3 75.3 - - - +
8K ALA* 1.3 57.5 + - - +
10K TYR* 3.2 2.4 + - - +
11K ILE* 2.9 39.3 + - - +
95K GLN* 3.8 16.4 - - - +
99K LEU* 3.7 31.4 - - + -
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Residues in contact with ALA 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237J GLN* 5.5 1.5 - - - +
4K VAL* 2.9 24.0 + - + +
5K ASN* 3.3 6.3 + - - +
7K THR* 1.3 76.0 + - - +
9K LEU* 1.3 59.4 + - + +
11K ILE* 3.3 9.2 + - - +
12K SER* 2.9 32.3 + - - -
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Residues in contact with LEU 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K ASN* 2.9 25.1 + - + +
6K ALA 4.0 0.7 - - - +
8K ALA* 1.3 74.6 - - + +
10K TYR* 1.3 58.9 + - - +
12K SER* 3.7 5.1 - - - -
13K ALA* 2.9 32.2 + - - +
34K LEU* 3.7 22.2 - - + +
37K TYR* 3.5 28.7 - - + +
38K PHE* 3.6 31.1 - - + +
41K SER* 3.5 18.4 - - - +
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Residues in contact with TYR 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I ILE* 3.5 22.2 - - - +
229I GLN* 3.0 29.2 + - + -
232I LEU* 4.9 9.0 - - + -
230J LEU* 3.9 13.5 - - + -
233J ILE* 5.1 2.0 - - + -
6K ALA 2.9 20.9 + - - +
7K THR* 3.2 4.9 + - - +
9K LEU* 1.3 74.5 - - - +
11K ILE* 1.3 63.7 + - + +
14K SER* 2.9 50.4 + - - -
38K PHE* 3.5 30.0 - + + -
99K LEU* 4.0 18.8 - - + -
102K CYS* 3.5 44.8 - - + -
106K LEU* 4.6 6.3 - - + -
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Residues in contact with ILE 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230J LEU* 4.4 24.2 - - + +
233J ILE* 4.0 17.3 - - + -
234J GLU* 3.7 38.4 - - + +
237J GLN* 4.9 6.1 - - + -
7K THR 2.9 24.2 + - - +
8K ALA* 3.7 8.3 - - - +
10K TYR* 1.3 78.5 - - + +
12K SER* 1.3 62.9 + - - +
15K ARG* 2.9 68.7 + - + +
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Residues in contact with SER 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ALA 2.9 18.5 + - - -
9K LEU* 3.7 7.4 - - - -
11K ILE* 1.3 76.6 - - - +
13K ALA* 1.3 57.7 + - - +
15K ARG* 3.9 3.0 - - - +
16K LEU* 3.0 38.6 + - - +
34K LEU* 3.6 23.1 - - - -
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Residues in contact with ALA 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K LEU 2.9 21.6 + - - +
10K TYR 3.9 2.2 - - - +
12K SER* 1.3 71.6 - - - +
14K SER* 1.3 60.0 + - - +
16K LEU* 3.1 4.8 + - - +
17K VAL* 2.9 35.1 + - - +
31K ILE* 6.4 0.2 - - - -
34K LEU* 4.0 15.7 - - + +
35K LEU* 4.2 16.6 - - + -
38K PHE* 4.0 23.1 - - + -
106K LEU* 4.3 7.0 - - + -
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Residues in contact with SER 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225I ILE* 4.8 0.3 - - - +
229I GLN* 4.5 1.2 + - - -
230J LEU* 3.6 25.1 - - - +
10K TYR* 2.9 47.7 + - - -
11K ILE 4.1 0.2 - - - -
13K ALA* 1.3 72.8 - - - +
15K ARG* 1.3 58.3 + - - +
17K VAL* 3.5 0.7 + - - +
18K LEU* 2.9 41.1 + - - +
106K LEU* 3.4 24.1 - - - +
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Residues in contact with ARG 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227J LEU* 4.2 20.9 - - + -
230J LEU* 4.1 9.9 - - + +
231J ASP* 2.7 42.8 + - - +
234J GLU* 2.6 36.7 + - - +
11K ILE* 2.9 39.7 + - + +
12K SER* 3.9 4.3 - - - +
14K SER* 1.3 76.9 - - - +
16K LEU* 1.3 62.1 + - + +
19K ASN* 3.0 43.4 + - - +
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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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12K SER* 3.0 29.1 + - - +
13K ALA* 3.1 6.0 + - - +
15K ARG* 1.3 83.1 - - + +
17K VAL* 1.3 60.7 + - - +
19K ASN* 4.2 2.1 - - - -
20K TYR* 3.7 12.8 + - - -
27K ALA* 5.9 0.6 - - - +
30K GLU* 3.5 49.4 - - + +
31K ILE* 3.4 23.7 - - + +
34K LEU* 3.7 20.6 - - + -
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Residues in contact with VAL 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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13K ALA 2.9 21.3 + - - +
14K SER* 3.9 5.4 - - - +
16K LEU* 1.3 77.2 - - - +
18K LEU* 1.3 62.4 + - + +
20K TYR* 3.3 20.1 + - - +
31K ILE* 4.0 24.7 - - + -
35K LEU* 4.9 2.0 - - + -
106K LEU* 4.5 9.0 - - + -
109K TYR* 3.9 25.5 + - + -
110K ILE* 3.8 37.2 - - + -
115K LEU* 3.8 18.5 - - + +
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Residues in contact with LEU 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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222I LEU* 4.0 7.4 - - + -
223J LYS* 4.0 39.1 - - + +
226J LEU* 3.3 40.8 - - + -
227J LEU* 3.7 23.1 - - + +
230J LEU* 4.1 12.3 - - + -
14K SER* 2.9 31.4 + - - +
17K VAL* 1.3 80.0 - - + +
19K ASN* 1.3 61.4 + - - +
20K TYR 3.3 1.5 + - - -
106K LEU* 5.2 5.6 - - + -
109K TYR* 4.1 20.9 - - + +
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Residues in contact with ASN 19 (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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227J LEU* 3.7 30.7 - - - +
15K ARG* 3.0 30.1 + - - +
16K LEU* 4.2 3.4 - - - +
18K LEU* 1.3 77.0 - - - +
20K TYR* 1.3 65.7 + - - +
21K ASP* 2.8 10.7 + - - +
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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
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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