Contacts of the helix formed by residues 7 - 21 (chain A) in PDB entry 1YQS
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ALA 3.5 0.2 + - - -
6A PRO* 1.3 72.5 - - - +
8A ASP* 1.3 57.4 + - - +
9A THR* 3.2 4.6 + - - -
10A GLY* 3.0 27.3 + - - -
11A LEU* 2.9 30.3 + - - +
341A SER* 3.0 22.0 + - - +
342A ALA* 4.7 0.2 - - - +
345A GLY 3.8 3.0 - - - +
346A LYS* 2.9 62.2 + - + +
347A PRO* 4.6 4.2 - - - +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 3.7 2.9 + - - +
7A ASP* 1.3 69.3 + - - +
9A THR* 1.3 61.5 + - - +
11A LEU* 3.3 14.3 + - - +
12A GLN* 2.8 30.2 + - - +
37A HIS* 2.7 42.2 + - - +
38A GLN 5.4 0.2 + - - -
39A LEU* 3.7 23.4 - - + +
346A LYS* 4.5 2.8 - - - +
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 3.2 8.8 + - - -
8A ASP* 1.3 77.0 - - - +
10A GLY* 1.3 63.9 + - - +
12A GLN* 3.3 12.4 + - + +
13A ALA* 3.1 22.7 + - + +
346A LYS* 4.6 12.9 + - - +
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Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ASP* 3.0 27.1 + - - -
9A THR* 1.3 75.1 - - - +
11A LEU* 1.3 65.6 + - - +
13A ALA* 3.2 8.3 + - - +
14A VAL* 3.0 25.6 + - - +
337A ARG* 4.8 0.7 + - - -
341A SER* 3.5 13.7 - - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PRO* 5.2 1.1 - - + -
7A ASP 2.9 17.5 + - - +
8A ASP* 3.6 27.4 - - - +
10A GLY* 1.3 77.2 - - - +
12A GLN* 1.3 62.1 + - - +
14A VAL* 3.1 6.0 + - - +
15A LEU* 3.0 28.8 + - - +
28A VAL* 4.1 21.1 - - + -
30A VAL* 4.1 22.9 - - + -
37A HIS* 5.1 0.4 - - + -
39A LEU* 4.2 14.1 - - + -
338A THR* 3.6 44.0 - - + +
341A SER* 3.8 11.6 + - - -
342A ALA* 4.2 7.4 - - + +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASP 2.8 20.7 + - - +
9A THR* 3.5 11.2 - - - +
11A LEU* 1.3 72.7 - - - +
13A ALA* 1.3 55.9 + - - +
15A LEU* 3.3 7.1 + - - +
16A HIS* 3.0 29.7 + - + +
39A LEU* 3.8 20.5 - - + +
41A GLU* 4.4 4.9 - - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 3.1 13.2 + - + +
10A GLY* 3.2 11.6 + - - +
12A GLN* 1.3 76.2 - - - +
14A VAL* 1.3 58.1 + - - +
16A HIS* 3.3 6.1 + - - +
17A THR* 2.9 35.0 + - - +
337A ARG* 4.2 11.0 - - - +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY 3.0 19.4 + - - +
11A LEU* 3.1 8.3 + - - +
13A ALA* 1.3 76.2 - - - +
15A LEU* 1.3 63.5 + - - +
17A THR 3.2 1.4 + - - -
18A ALA* 2.9 19.2 + - - +
334A THR* 3.3 34.3 - - + +
335A MET* 4.3 5.6 - - - -
337A ARG* 3.6 47.3 - - + +
338A THR* 3.7 24.2 - - + +
341A SER* 4.2 6.5 - - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 3.0 13.8 + - - +
12A GLN* 3.8 7.0 - - - +
14A VAL* 1.3 76.7 - - - +
16A HIS* 1.3 65.0 + - - +
18A ALA* 3.2 6.6 + - - +
19A LEU* 3.0 27.8 + - - +
26A ALA* 3.7 26.2 - - + +
27A MET* 3.8 24.2 - - - +
28A VAL* 4.3 9.6 - - + -
39A LEU* 3.7 39.9 - - + +
40A SER* 3.8 7.0 - - - +
41A GLU* 4.1 10.1 - - + +
335A MET* 4.1 15.7 - - + -
338A THR* 4.6 5.2 - - + -
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Residues in contact with HIS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLN* 3.0 19.0 + - + +
13A ALA* 3.7 7.6 - - - +
14A VAL 3.2 0.2 - - - -
15A LEU* 1.3 77.6 - - - +
17A THR* 1.3 62.9 + - - +
19A LEU* 3.3 6.8 + - + +
20A SER* 3.0 24.6 + - - -
41A GLU* 2.9 36.8 + - - +
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 2.9 19.2 + - - +
14A VAL 3.2 4.2 + - - -
16A HIS* 1.3 78.9 - - - +
18A ALA* 1.3 62.0 + - - +
20A SER* 2.7 27.9 + - - +
21A GLN* 3.1 30.2 + - - +
334A THR* 3.8 6.3 - - + +
337A ARG* 3.5 26.4 + - - +
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL 2.9 13.3 + - - +
15A LEU 3.2 8.7 + - - +
17A THR* 1.3 75.3 - - - +
19A LEU* 1.3 63.8 + - - +
21A GLN* 3.1 13.9 + - - -
22A GLY 3.2 1.2 + - - -
23A ALA* 3.1 26.9 + - + +
26A ALA* 4.1 8.7 - - + -
331A VAL* 3.7 10.0 - - + +
334A THR* 3.7 9.8 - - + +
335A MET* 3.7 27.4 - - - -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 3.0 18.4 + - - +
16A HIS* 3.6 9.9 - - + +
18A ALA* 1.3 76.0 - - - +
20A SER* 1.3 61.8 + - - +
22A GLY* 3.1 14.0 + - - -
23A ALA 3.4 22.0 - - - +
24A PRO 4.1 3.8 - - - +
25A GLY 4.0 1.1 - - - -
26A ALA* 3.8 18.8 - - + +
41A GLU* 3.6 52.0 - - + +
42A GLY* 3.8 15.5 - - - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A HIS* 3.0 14.8 + - - -
17A THR* 2.7 26.6 + - - +
19A LEU* 1.3 76.0 - - - +
21A GLN* 1.3 62.5 + - - +
22A GLY 3.5 0.2 - - - -
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Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 3.1 25.6 + - + +
18A ALA* 3.6 5.9 - - - +
19A LEU 3.1 0.6 - - - -
20A SER* 1.3 82.5 - - - +
22A GLY* 1.3 56.3 + - - +
328A ASN* 2.9 21.0 + - - +
330A ASN* 3.2 39.6 + - + +
331A VAL* 3.8 10.6 + - + -
334A THR* 2.6 33.7 + - - +
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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
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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