Contacts of the helix formed by residues 4 - 23 (chain I) in PDB entry 4LLL
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 4 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE* 1.3 94.8 - - + +
5I TYR* 1.3 63.7 + - - +
6I SER* 3.4 10.3 + - - +
7I TYR* 3.1 32.8 + - + +
8I LEU* 3.2 12.4 + - - +
112J GLU* 3.1 26.9 + - - +
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Residues in contact with TYR 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE 3.4 6.5 + - - -
4I THR* 1.3 66.6 - - - +
6I SER* 1.3 57.4 + - - +
7I TYR 2.8 11.1 + - - -
8I LEU* 2.9 21.1 + - + +
9I PHE* 2.9 18.5 + - + +
16J MET* 5.1 1.1 - - + -
112J GLU* 2.7 16.5 + - - +
115J LEU* 4.2 23.8 - - + -
116J VAL* 3.5 49.6 - - + -
119J LEU* 5.6 0.2 - - - +
124J ASN* 3.4 36.0 + - + +
127J MET* 4.7 17.2 - - + +
128J LYS* 4.8 21.5 - - + -
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Residues in contact with SER 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I THR* 3.4 15.1 + - - +
5I TYR* 1.3 76.7 - - - +
7I TYR* 1.3 58.5 + - - +
9I PHE* 4.5 1.3 - - - +
10I ARG* 3.6 18.5 + - - +
16J MET* 3.6 31.6 - - - +
35J HIS* 4.3 28.4 + - - -
108J PHE* 5.0 9.8 + - - +
111J MET* 6.2 1.6 - - - -
112J GLU* 3.6 6.7 + - - -
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Residues in contact with TYR 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE* 4.2 33.4 - + + -
4I THR* 3.1 28.2 + - + +
5I TYR 2.8 1.2 + - - -
6I SER* 1.3 81.1 + - - +
8I LEU* 1.3 71.8 + - + +
9I PHE 3.2 0.2 - - - -
10I ARG* 3.2 4.5 + - - +
11I MET* 3.0 61.1 + - + +
56J ALA 4.4 15.9 + - - -
57J LEU* 6.0 4.5 - - + -
58J GLN* 6.0 0.5 - - - +
135J LEU* 5.3 6.5 - - + -
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Residues in contact with LEU 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE* 5.4 5.2 - - + +
4I THR 3.2 7.7 + - - +
5I TYR* 2.9 13.9 + - + +
7I TYR* 1.3 90.2 - - + +
9I PHE* 1.3 58.3 + - - +
11I MET* 4.3 2.1 - - - +
12I ILE* 3.1 30.3 + - - +
128J LYS* 6.5 1.1 - - - -
131J LEU* 4.9 17.9 - - + +
135J LEU* 4.7 9.3 - - + +
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Residues in contact with PHE 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 2.9 14.2 + - + +
6I SER* 5.1 0.4 - - - -
8I LEU* 1.3 75.4 - - - +
10I ARG* 1.3 65.3 + - - +
12I ILE* 3.9 3.8 - - - +
13I SER* 3.0 26.7 + - - -
9J PHE* 5.0 13.1 - - + +
12J ILE* 4.5 22.4 - - + -
13J SER* 4.1 8.7 - - - +
16J MET* 4.6 11.7 - - - -
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Residues in contact with ARG 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I SER 3.6 18.9 + - - +
7I TYR* 3.2 5.8 + - - +
9I PHE* 1.3 79.1 - - - +
11I MET* 1.3 72.5 + - + +
13I SER* 2.7 22.2 + - - -
14I HIS* 3.1 11.8 + - - +
13J SER* 3.8 11.1 + - - +
59J ARG* 4.5 2.0 + - - +
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Residues in contact with MET 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I TYR* 3.0 54.9 + - + +
8I LEU 4.3 0.2 - - - +
10I ARG* 1.3 85.6 - - + +
12I ILE* 1.3 63.9 + - - +
14I HIS* 3.3 4.6 + - - +
15I GLU* 3.2 29.5 + - + +
57J LEU* 3.8 24.2 - - + +
58J GLN* 3.9 17.3 - - - -
59J ARG* 3.2 31.9 - - - +
135J LEU* 4.1 19.7 - - + -
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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
----------------------------------------------------------
8I LEU 3.1 21.2 + - - +
9I PHE* 3.9 4.7 - - - +
10I ARG 3.3 0.4 - - - -
11I MET* 1.3 76.9 - - - +
13I SER* 1.3 64.3 + - - +
14I HIS 3.3 0.5 + - - -
15I GLU* 3.7 2.7 + - - +
16I MET* 3.1 29.1 + - + +
9J PHE* 4.9 23.1 - - + -
131J LEU* 6.2 3.4 - - + -
134J MET* 6.5 1.1 - - + -
135J LEU* 4.6 19.0 - - + +
138J LEU* 5.7 0.3 - - - +
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Residues in contact with SER 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I PHE 3.0 11.7 + - - -
10I ARG 2.7 20.8 + - - -
12I ILE* 1.3 77.7 - - - +
14I HIS* 1.3 66.0 + - - +
16I MET* 3.4 12.3 + - - +
17I LYS* 3.2 22.2 + - - +
9J PHE* 3.9 16.7 - - - +
10J ARG* 4.9 3.4 - - - -
13J SER* 3.0 28.7 + - - -
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Residues in contact with HIS 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ARG 3.3 14.6 - - - +
11I MET* 3.5 6.5 - - - +
12I ILE 3.2 0.2 - - - -
13I SER* 1.3 82.6 + - - +
15I GLU* 1.3 73.8 + - - +
17I LYS* 3.2 7.6 + - + +
18I GLN* 2.9 59.9 + - + -
58J GLN* 3.3 16.8 + - - +
59J ARG* 3.1 48.4 + - - +
60J THR* 6.6 0.2 - - + -
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Residues in contact with GLU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I MET* 3.2 16.7 + - + +
12I ILE* 4.5 2.2 - - - +
14I HIS* 1.3 94.3 + - - +
16I MET* 1.3 53.2 + - - +
18I GLN* 3.0 13.0 + - - +
19I LYS* 2.6 37.6 + - - +
58J GLN* 2.3 39.2 + - + +
135J LEU* 6.0 5.2 - - + -
138J LEU* 3.6 35.3 - - + +
139J GLN* 4.4 16.5 - - + +
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Residues in contact with MET 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 3.1 18.4 + - - +
13I SER* 3.4 8.3 - - - +
15I GLU* 1.3 74.0 - - - +
17I LYS* 1.3 59.9 + - - +
19I LYS* 4.1 4.5 - - - +
20I ALA* 2.9 32.1 + - - +
31I ASN* 5.1 0.7 - - - -
111I MET* 5.7 10.8 - - + +
5J TYR* 5.5 1.8 - - + -
6J SER* 3.7 37.0 - - - +
9J PHE* 3.6 35.4 - - + -
138J LEU* 4.7 8.0 - - + +
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Residues in contact with LYS 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I SER 3.2 10.3 + - - +
14I HIS* 3.2 10.3 + - + +
16I MET* 1.3 79.8 - - - +
18I GLN* 1.3 60.9 + - - +
20I ALA* 3.7 0.9 - - - +
21I ASP* 2.9 38.2 + - - +
31I ASN* 3.5 29.0 - - + +
32I GLU* 4.9 7.0 - - - +
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Residues in contact with GLN 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I HIS* 2.9 54.2 + - + +
15I GLU* 3.0 21.3 + - - +
17I LYS* 1.3 76.8 - - - +
19I LYS* 1.3 66.9 + - - +
21I ASP* 2.8 30.7 + - - +
22I GLN* 2.9 14.7 + - - +
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Residues in contact with LYS 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I GLU* 2.6 18.9 + - - +
16I MET* 4.1 4.7 - - - +
18I GLN* 1.3 72.9 - - - +
20I ALA* 1.3 61.9 + - - +
22I GLN* 3.5 7.4 + - - +
23I LYS* 3.0 24.7 + - - +
138J LEU* 5.4 10.8 - - + +
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Residues in contact with ALA 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I MET 2.9 19.7 + - - +
17I LYS 3.7 2.7 - - - +
19I LYS* 1.3 74.1 - - - +
21I ASP* 1.3 68.2 + - - +
23I LYS* 3.1 13.6 + - - +
24I LEU* 3.1 22.1 + - + +
31I ASN* 3.4 26.5 - - + +
107I ILE* 5.1 7.2 - - + -
108I PHE* 4.6 13.5 - - + -
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Residues in contact with ASP 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I LYS* 2.9 22.2 + - - +
18I GLN* 2.8 24.7 + - - +
20I ALA* 1.3 75.6 - - - +
22I GLN* 1.3 62.6 + - - +
24I LEU* 2.9 17.7 + - - +
25I GLU* 3.2 12.5 + - - +
29I ILE 4.8 1.5 - - - +
30I THR* 3.6 8.8 - - - -
31I ASN* 2.8 33.3 + - - +
32I GLU* 4.7 1.6 - - - +
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLN 2.9 10.8 + - - +
19I LYS* 3.7 10.5 - - - +
21I ASP* 1.3 77.0 - - - +
23I LYS* 1.3 58.4 + - - +
24I LEU 2.9 5.5 + - - -
25I GLU* 3.3 16.6 + - - +
26I GLN* 5.4 0.7 + - - +
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Residues in contact with LYS 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LYS 3.0 17.5 + - - +
20I ALA 3.1 4.0 + - - +
22I GLN* 1.3 74.6 - - - +
24I LEU* 1.3 57.9 + - - +
25I GLU 3.7 0.2 - - - -
26I GLN* 3.1 27.2 + - - +
107I ILE* 3.2 34.6 - - + +
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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