Contacts of the helix formed by residues 1 - 19 (chain A) in PDB entry 1T6S
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 MET 1 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLN* 1.3 66.8 + - + +
3A GLU* 3.4 4.6 + - - +
4A GLN* 3.9 23.4 - - + +
5A ARG* 3.0 28.9 + - - +
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Residues in contact with GLN 2 (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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1A MET* 1.3 83.6 - - + +
3A GLU* 1.3 64.2 + - - +
5A ARG* 3.1 3.1 + - - -
6A GLN* 2.8 54.4 + - + +
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Residues in contact with GLU 3 (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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1A MET 3.4 2.1 + - - +
2A GLN* 1.3 92.7 + - - +
4A GLN* 1.3 52.7 + - - +
6A GLN* 3.1 9.3 + - + +
7A GLN* 2.8 36.3 + - - +
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Residues in contact with GLN 4 (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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1A MET* 3.6 26.1 + - - +
2A GLN 3.3 0.4 - - - -
3A GLU* 1.3 74.9 - - - +
5A ARG* 1.3 60.2 - - - +
7A GLN* 3.3 6.3 + - - +
8A LEU* 2.9 37.7 + - + +
34A HIS* 5.9 5.5 + - - -
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Residues in contact with ARG 5 (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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1A MET 3.0 20.3 + - - +
2A GLN* 3.3 6.3 - - - +
4A GLN* 1.3 76.7 - - - +
6A GLN* 1.3 78.0 + - - +
8A LEU* 3.2 14.5 + - + +
9A LEU* 2.9 55.2 + - - +
36A PHE* 6.1 1.0 - - - -
40A GLU* 6.3 1.8 - - - +
43A GLU* 4.3 13.7 + - - +
44A ALA* 4.1 19.8 - - - +
47A GLU* 3.0 28.3 + - - -
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Residues in contact with GLN 6 (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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2A GLN* 2.8 43.4 + - + +
3A GLU* 3.1 9.4 + - + +
5A ARG* 1.3 99.4 - - - +
7A GLN* 1.3 56.9 + - - +
9A LEU* 3.3 10.5 + - - +
10A ARG* 2.9 38.1 + - - +
47A GLU* 4.0 15.0 + - - +
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Residues in contact with GLN 7 (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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3A GLU 2.8 19.5 + - - +
4A GLN* 3.8 7.2 - - - +
6A GLN* 1.3 70.0 - - - +
8A LEU* 1.3 61.1 + - - +
10A ARG* 3.2 30.1 + - - +
11A SER* 2.9 40.5 + - - +
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Residues in contact with LEU 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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4A GLN* 2.9 24.2 + - + +
5A ARG* 3.5 14.1 - - + +
7A GLN* 1.3 76.4 - - - +
9A LEU* 1.3 63.2 + - + +
11A SER* 3.3 5.8 + - - +
12A LEU* 3.0 28.8 + - + +
32A THR* 3.8 32.1 - - + +
34A HIS* 3.7 41.3 - - + +
36A PHE* 4.0 22.0 - - + -
40A GLU* 5.3 1.1 - - - +
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Residues in contact with LEU 9 (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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5A ARG* 2.9 44.2 + - - +
6A GLN* 3.5 13.2 - - - +
7A GLN 3.2 0.2 - - - -
8A LEU* 1.3 79.3 - - + +
10A ARG* 1.3 62.1 + - + +
12A LEU* 3.2 9.5 + - + +
13A GLU* 3.0 21.7 + - - +
44A ALA* 3.4 30.5 - - + +
47A GLU* 3.3 42.2 - - + +
48A LEU* 3.8 28.2 - - + +
51A ASP* 5.0 2.9 - - - +
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Residues in contact with ARG 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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6A GLN* 2.9 22.1 + - - +
7A GLN* 3.2 30.2 + - - +
9A LEU* 1.3 77.2 - - + +
11A SER* 1.3 56.6 + - - +
13A GLU* 3.3 15.4 + - - +
14A ALA* 3.0 28.9 + - - +
48A LEU* 5.6 1.1 - - + -
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Residues in contact with SER 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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7A GLN* 2.9 24.8 + - - +
8A LEU* 3.6 11.6 - - - -
10A ARG* 1.3 75.0 - - - +
12A LEU* 1.3 65.5 + - - +
14A ALA* 3.3 6.0 + - - +
15A LEU* 3.0 31.8 + - - +
32A THR* 4.3 17.7 - - - -
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Residues in contact with LEU 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 LEU* 3.0 19.4 + - + +
9A LEU* 3.5 11.4 - - + +
11A SER* 1.3 76.3 - - - +
13A GLU* 1.3 64.1 + - - +
15A LEU* 3.2 4.6 + - - +
16A ILE* 2.9 34.8 + - + +
28A LEU* 4.1 33.4 - - + -
32A THR* 4.5 7.4 - - + -
36A PHE* 3.6 35.4 - - + -
41A LEU* 4.1 10.3 - - + -
44A ALA* 3.6 32.5 - - + -
45A VAL* 5.2 1.3 - - + +
48A LEU* 4.5 8.1 - - + -
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Residues in contact with GLU 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 LEU 3.0 12.0 + - - +
10A ARG* 3.5 17.0 + - - +
12A LEU* 1.3 76.9 - - - +
14A ALA* 1.3 54.8 + - - +
16A ILE* 3.4 4.4 + - - +
17A PHE* 2.7 42.4 + - + +
48A LEU* 4.0 18.6 - - + +
52A TYR* 2.7 40.9 + - - +
70A PHE* 4.0 9.0 - - + -
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Residues in contact with ALA 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 ARG 3.0 16.5 + - - +
11A SER* 3.7 7.4 - - - +
13A GLU* 1.3 79.2 - - - +
15A LEU* 1.3 58.4 + - + +
17A PHE* 3.9 5.0 - - - +
18A SER* 2.8 37.4 + - - +
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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 SER* 3.0 20.6 + - - +
12A LEU 3.8 0.7 - - - +
14A ALA* 1.3 74.4 - - + +
16A ILE* 1.3 66.0 + - - +
18A SER* 3.3 4.6 + - - -
19A SER* 3.0 25.7 + - - -
23A VAL* 4.3 5.3 - - + +
28A LEU* 3.7 25.4 - - + +
31A ILE* 3.9 42.0 - - + -
32A THR* 3.6 31.2 - - + -
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Residues in contact with ILE 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 LEU* 2.9 28.2 + - + +
13A GLU 4.0 1.8 - - - +
15A LEU* 1.3 75.2 - - - +
17A PHE* 1.3 60.0 + - - +
19A SER* 2.5 24.7 + - - +
23A VAL* 4.0 7.2 - - + -
28A LEU* 4.2 26.0 - - + -
45A VAL* 4.5 12.8 - - + -
48A LEU* 5.3 0.7 - - + -
61A ILE* 4.1 24.0 - - + -
68A TYR* 3.9 35.2 - - + +
69A ARG* 4.0 9.4 - - - +
70A PHE* 3.7 25.7 + - + -
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Residues in contact with PHE 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 GLU* 2.7 30.2 + - + +
14A ALA* 3.9 5.6 - - - +
16A ILE* 1.3 77.4 - - - +
18A SER* 1.3 67.4 + - - +
19A SER 4.1 4.0 - - - +
59A PHE* 5.3 16.4 - + - -
70A PHE* 3.6 31.6 - + + -
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Residues in contact with SER 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 ALA* 2.8 26.3 + - - +
15A LEU* 3.3 5.6 + - - -
17A PHE* 1.3 81.5 - - - +
19A SER* 1.3 66.1 + - - +
20A GLU* 3.5 14.0 + - - +
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Residues in contact with SER 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 9.2 + - - -
16A ILE* 2.5 25.1 + - - +
17A PHE 3.3 4.9 - - - +
18A SER* 1.3 78.9 - - - +
20A GLU* 1.3 57.3 + - - +
21A GLU 3.1 25.4 + - - -
23A VAL* 3.3 20.5 - - - +
68A TYR 4.7 1.9 + - - -
69A ARG* 5.3 3.1 - - - +
403A NO3 3.3 13.2 - - - -
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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