Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 1SQU
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 ASP 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 75.9 - - - +
3B ALA* 1.3 66.8 + - - +
4B ARG* 2.6 48.1 + - - +
5B ILE* 2.8 41.1 + - + +
6B VAL* 3.0 13.8 + - - +
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Residues in contact with ALA 3 (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 3.4 4.0 + - - -
2B ASP* 1.3 74.6 + - - +
4B ARG* 1.3 56.8 + - + +
6B VAL* 3.5 12.1 - - + +
7B ASN* 2.5 51.4 + - - +
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Residues in contact with ARG 4 (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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2B ASP* 2.6 30.8 + - - +
3B ALA* 1.3 79.3 - - + +
5B ILE* 1.3 56.0 + - + +
7B ASN* 3.3 8.4 + - - +
8B ALA* 2.6 36.5 + - - +
107B LEU* 3.3 59.5 + - + +
109B LYS* 4.4 20.2 - - - +
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Residues in contact with ILE 5 (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 22.2 - - + -
2B ASP* 2.8 29.5 + - + +
4B ARG* 1.3 81.1 - - + +
6B VAL* 1.3 53.9 + - - +
8B ALA* 2.9 8.8 + - - +
9B LEU* 2.8 33.1 + - + +
52B ILE* 5.3 12.6 - - + -
100B LEU* 4.7 2.8 - - + +
104B LEU* 4.5 20.6 - - + -
107B LEU* 5.0 0.9 - - + +
109B LYS* 5.6 9.0 - - + -
149B LEU* 3.9 26.5 - - + -
151B VAL* 5.5 5.4 - - + -
154B GLY 5.1 15.9 - - - +
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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
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1B MET* 3.3 29.6 - - + +
2B ASP 3.0 15.8 + - - +
3B ALA* 3.1 13.7 + - + +
5B ILE* 1.3 75.4 - - - +
7B ASN* 1.3 62.8 + - - +
9B LEU* 3.4 7.0 + - + +
10B ILE* 3.1 34.0 + - + +
30B PRO* 3.6 37.7 - - + -
133B LEU* 4.3 15.3 - - + -
135B LEU* 5.7 0.9 - - + -
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 2.5 34.1 + - - +
4B ARG* 3.6 7.9 - - - +
6B VAL* 1.3 74.4 - - - +
8B ALA* 1.3 66.1 + - - +
9B LEU 3.2 0.2 + - - -
10B ILE* 3.2 16.9 + - - +
11B GLY* 2.9 22.9 + - - -
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Residues in contact with ALA 8 (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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4B ARG 2.6 22.7 + - - +
5B ILE* 2.9 9.4 + - - +
7B ASN* 1.3 72.7 - - - +
9B LEU* 1.3 56.1 + - - +
12B SER* 2.7 33.1 + - - -
100B LEU* 3.5 13.8 - - + +
103B LYS* 3.8 25.7 - - + +
104B LEU* 4.1 13.0 - - + -
107B LEU* 5.2 5.4 - - + -
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Residues in contact with LEU 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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5B ILE 2.8 11.8 + - - +
6B VAL* 3.6 9.9 - - + +
8B ALA* 1.3 74.7 - - - +
10B ILE* 1.3 67.6 + - - +
12B SER* 2.9 16.6 + - - -
13B VAL* 3.0 23.9 + - + +
56B LEU* 4.0 24.2 - - + -
96B THR* 5.4 0.7 - - + -
100B LEU* 3.5 26.8 - - + +
133B LEU* 3.9 24.7 - - + -
135B LEU* 4.0 14.4 - - + -
147B LEU* 3.7 24.0 - - + -
149B LEU* 4.1 16.6 - - + -
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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* 3.1 30.5 + - + +
7B ASN* 3.5 18.2 - - - +
9B LEU* 1.3 79.0 - - - +
11B GLY* 1.3 65.5 + - - +
13B VAL* 3.2 3.4 + - - +
14B TYR* 2.9 24.9 + - + +
27B THR* 3.9 33.0 - - + +
30B PRO* 4.4 13.2 - - + -
135B LEU* 4.0 29.4 - - + -
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN 2.9 14.5 + - - -
8B ALA 4.2 1.1 - - - -
10B ILE* 1.3 79.4 - - - +
12B SER* 1.3 56.7 + - - +
14B TYR* 4.3 4.9 - - - -
15B GLU* 2.9 44.3 + - - +
103B LYS* 4.3 11.0 - - - -
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Residues in contact with SER 12 (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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8B ALA 2.7 20.0 + - - -
9B LEU* 2.9 9.3 + - - -
11B GLY* 1.3 71.4 - - - +
13B VAL* 1.3 60.7 + - - +
16B THR* 2.8 36.6 + - - -
96B THR* 3.7 26.5 - - - -
99B LYS* 3.5 14.2 + - - -
100B LEU* 3.1 26.1 + - - -
103B LYS* 3.8 6.9 - - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.0 22.6 + - + +
10B ILE* 3.7 7.2 - - - +
12B SER* 1.3 73.4 - - - +
14B TYR* 1.3 66.5 + - - +
17B ILE* 2.8 45.0 + - + +
25B PRO* 4.9 4.0 - - + -
27B THR* 6.4 2.2 - - - -
96B THR* 3.9 19.3 - - + -
135B LEU* 4.4 3.8 - - + -
137B ILE* 3.5 33.7 - - + -
145B PHE* 6.5 0.4 - - + -
147B LEU* 3.6 25.8 - - + -
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Residues in contact with TYR 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 21.4 + - + +
11B GLY* 3.6 6.7 - - - +
13B VAL* 1.3 81.3 - - - +
15B GLU* 1.3 86.9 + - + +
18B ARG* 3.2 45.6 + - - +
24B GLU* 2.8 30.8 + - + +
25B PRO* 3.4 44.9 - - + +
27B THR* 5.2 11.7 - - + -
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Residues in contact with GLU 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 GLY* 2.9 26.0 + - - +
14B TYR* 1.3 85.1 - - + +
16B THR* 1.3 56.8 + - - +
18B ARG* 3.4 19.5 + - - +
19B ASP* 3.1 36.6 + - - +
99B LYS* 3.3 28.6 + - + +
103B LYS* 3.2 35.6 + - - -
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Residues in contact with THR 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 SER 2.8 24.4 + - - -
13B VAL 4.1 1.1 - - - -
15B GLU* 1.3 73.5 - - - +
17B ILE* 1.3 59.7 + - + +
18B ARG 2.9 5.2 + - - -
19B ASP* 3.2 2.3 + - - -
20B VAL* 2.9 43.7 + - + +
92B LEU* 4.0 15.9 - - + +
95B MET* 3.8 5.6 + - + -
96B THR* 3.6 36.3 - - - +
99B LYS* 2.9 26.1 - - - +
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Residues in contact with ILE 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 VAL* 2.8 36.4 + - + +
16B THR* 1.3 79.6 - - + +
18B ARG* 1.3 57.2 + - - +
21B LEU* 3.1 39.0 + - + +
22B GLY 3.5 0.5 + - - -
23B ILE* 2.9 34.1 - - + +
25B PRO* 3.2 38.4 - - + -
92B LEU* 4.7 9.9 - - + -
96B THR* 5.6 2.0 - - - +
137B ILE* 5.8 0.7 - - + -
139B VAL* 3.5 34.1 - - + -
145B PHE* 5.5 9.4 - - + -
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Residues in contact with ARG 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 TYR* 3.2 38.9 + - - +
15B GLU* 3.4 22.0 - - - +
16B THR 2.9 0.8 - - - -
17B ILE* 1.3 80.2 - - - +
19B ASP* 1.3 82.8 + - - +
22B GLY* 2.8 30.2 - - - -
23B ILE 3.3 11.7 - - - +
24B GLU* 3.8 31.0 - - + -
25B PRO* 4.6 2.0 - - + -
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Residues in contact with ASP 19 (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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15B GLU* 3.1 19.5 + - - +
16B THR* 4.1 2.5 - - - +
18B ARG* 1.3 107.9 + - - +
20B VAL* 1.3 64.3 + - + +
22B GLY* 4.4 1.7 + - - -
99B LYS* 4.2 17.2 + - - -
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Residues in contact with VAL 20 (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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16B THR* 2.9 27.2 + - + +
19B ASP* 1.3 85.2 - - + +
21B LEU* 1.3 61.6 + - - +
22B GLY 3.4 0.2 - - - -
71B ALA 3.8 2.4 - - - +
72B MET* 3.6 53.8 - - + +
92B LEU* 4.0 13.7 - - + -
95B MET* 3.6 36.1 - - + -
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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