Contacts of the helix formed by residues 2 - 18 (chain B) in PDB entry 3SJ5
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 LYS 2 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 79.1 - - + +
3B GLY* 1.3 66.5 + - - +
4B THR* 3.3 4.3 - - - +
5B PHE* 2.9 56.0 + - + +
6B VAL* 3.0 12.8 + - - +
41B GLU 4.4 2.5 - - - -
105B LEU 3.8 16.0 + - - -
106B THR* 4.2 7.6 - - - +
109B ILE* 3.3 34.2 - - - +
502B HEM 3.7 31.1 - - + +
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Residues in contact with GLY 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.9 2.0 + - - -
2B LYS* 1.3 70.7 - - - +
4B THR* 1.3 51.7 + - - +
6B VAL* 3.1 3.8 + - - +
7B GLY 2.6 31.4 + - - -
37B ILE* 3.4 28.1 - - - +
38B THR 5.0 0.4 - - - -
41B GLU 3.1 21.3 + - - -
43B ILE* 4.2 17.7 - - - -
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Residues in contact with THR 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 4.8 3.1 - - - +
3B GLY* 1.3 76.0 + - - +
5B PHE* 1.3 70.8 + - - +
7B GLY* 3.3 3.4 + - - +
8B THR* 2.9 32.7 + - - +
37B ILE* 4.6 8.7 - - + +
38B THR 4.0 17.4 + - - +
39B PRO* 4.0 18.8 + - + +
81B TRP* 4.0 8.8 - - - -
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Residues in contact with PHE 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.0 7.2 - - + -
2B LYS* 2.9 39.1 + - + +
4B THR* 1.3 85.1 + - - +
6B VAL* 1.3 61.6 + - - +
8B THR* 2.7 21.6 + - - -
9B TRP* 3.0 28.1 + + + +
78B PHE* 3.8 22.0 - + - -
81B TRP* 3.5 31.4 - + - -
82B PHE* 4.5 11.9 - + - -
140B TYR* 6.2 0.2 - - - -
502B HEM 3.3 48.2 - + + -
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Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.0 19.3 - - + -
2B LYS 3.0 12.6 + - - +
3B GLY 3.5 6.3 - - - +
5B PHE* 1.3 74.2 - - - +
7B GLY* 1.3 57.2 + - - +
9B TRP* 3.2 24.6 + - + +
10B ILE* 2.9 48.7 + - + +
31B TRP* 4.5 2.5 - - + -
43B ILE* 3.8 37.7 - - + -
48B VAL* 4.2 20.4 - - + -
51B ILE* 5.4 2.5 - - + -
52B PHE* 6.5 0.4 - - + -
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLY 2.6 19.4 + - - -
4B THR* 3.5 6.1 - - - -
5B PHE 3.1 0.2 - - - -
6B VAL* 1.3 74.6 - - - +
8B THR* 1.3 55.5 + - - +
10B ILE* 3.3 11.2 + - - +
11B LYS* 2.9 26.9 + - - +
37B ILE* 5.0 11.2 - - - +
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Residues in contact with THR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR 2.9 10.7 + - - +
5B PHE* 2.7 24.6 + - - -
7B GLY* 1.3 72.7 - - - +
9B TRP* 1.3 62.3 + - - +
11B LYS* 3.2 10.5 + - + +
12B THR* 2.8 34.6 + - - -
74B ASN* 4.1 16.6 + - - -
77B THR* 3.9 12.1 - - + -
78B PHE* 6.1 0.2 - - - -
81B TRP* 3.1 40.6 - - + -
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Residues in contact with TRP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.5 39.3 - - + -
5B PHE* 3.0 26.9 + + + +
6B VAL* 3.2 34.7 + - + +
8B THR* 1.3 78.5 + - - +
10B ILE* 1.3 57.2 + - + +
12B THR* 3.1 8.8 + - - -
13B LEU* 2.9 31.9 + - - +
48B VAL* 4.2 14.8 - - + -
52B PHE* 4.3 15.0 - + + -
67B TRP* 3.7 23.3 - + - -
70B VAL* 3.6 15.9 - - + +
74B ASN* 2.9 33.4 - - - +
137B MET* 3.7 10.8 - - + -
140B TYR* 3.1 28.0 + + - -
502B HEM 5.2 3.8 - - + -
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 2.9 31.5 + - + +
7B GLY* 3.6 10.8 - - - +
9B TRP* 1.3 77.0 - - + +
11B LYS* 1.3 61.8 + - - +
13B LEU* 3.1 17.0 + - + +
14B ARG* 2.9 36.7 + - - +
22B VAL* 3.5 26.9 - - + -
26B LEU* 4.1 19.3 - - + -
31B TRP* 3.8 29.2 - - + -
37B ILE* 5.6 4.7 - - + -
51B ILE* 4.8 7.6 - - + -
52B PHE* 6.0 1.6 - - + -
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLY 2.9 14.6 + - - +
8B THR* 3.4 14.8 - - + +
10B ILE* 1.3 75.2 - - - +
12B THR* 1.3 59.1 + - - +
14B ARG* 3.1 17.0 + - - +
15B ASP* 2.7 43.3 + - - +
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR 2.8 19.6 + - - -
9B TRP* 3.3 12.2 - - - -
11B LYS* 1.3 74.6 - - - +
13B LEU* 1.3 62.1 + - - +
15B ASP* 3.1 9.7 + - - +
16B LEU* 3.0 44.6 + - + +
70B VAL* 3.7 27.7 + - + +
73B GLN* 4.1 23.1 - - + +
74B ASN* 5.0 5.7 + - - -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TRP 2.9 18.5 + - - +
10B ILE* 3.1 15.9 + - + +
12B THR* 1.3 75.6 - - - +
14B ARG* 1.3 58.5 + - - +
16B LEU* 4.8 0.2 - - - -
17B TYR* 2.8 53.0 + - + +
18B GLY 3.6 0.2 + - - -
22B VAL* 3.6 14.7 - - + +
51B ILE* 4.5 9.9 - - + -
52B PHE* 4.0 27.6 - - + -
55B VAL* 4.2 21.5 - - + -
66B ILE* 3.6 31.2 - - + -
70B VAL* 4.0 12.8 - - + -
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 2.9 27.0 + - - +
11B LYS* 3.1 19.7 + - + +
13B LEU* 1.3 76.5 - - - +
15B ASP* 1.3 61.4 + - - +
18B GLY* 2.7 30.9 + - - +
19B ASN* 2.9 40.7 + - - +
22B VAL* 3.6 23.0 - - + +
23B ASP* 2.8 29.5 + - - -
26B LEU* 3.5 17.8 - - - +
33B PRO 3.3 24.9 + - - -
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 2.7 31.5 + - - +
12B THR* 3.1 9.9 + - + +
14B ARG* 1.3 82.7 - - - +
16B LEU* 1.3 67.2 + - + +
17B TYR 3.4 0.3 + - - -
18B GLY* 4.4 1.0 + - - -
73B GLN* 5.4 5.7 - - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B THR* 3.0 34.2 + - + +
15B ASP* 1.3 79.8 - - + +
17B TYR* 1.3 98.0 + - + +
69B GLU* 3.5 30.3 - - + +
70B VAL* 4.6 6.3 - - + -
73B GLN* 3.5 32.3 - - - +
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Residues in contact with TYR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 2.8 44.9 + - + +
15B ASP 4.8 0.2 - - - -
16B LEU* 1.3 119.9 - - + +
18B GLY* 1.3 58.6 + - - +
21B VAL* 3.8 25.0 - - + +
22B VAL* 5.2 0.7 - - + -
55B VAL* 3.5 22.7 - - + -
59B THR* 4.3 21.3 - - + -
61B LYS* 4.9 16.4 - - + +
65B GLU 5.2 0.2 + - - -
66B ILE* 3.5 36.7 - - + +
69B GLU* 4.9 4.2 - - - +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 2.7 26.8 + - - -
15B ASP 4.4 1.0 + - - -
17B TYR* 1.3 76.0 - - - +
19B ASN* 1.3 65.8 + - - -
20B ASP 3.3 2.9 - - - -
21B VAL 3.7 1.2 + - - -
22B VAL* 3.3 26.0 + - - +
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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