Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 1TDH
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 GLU 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PRO* 1.3 82.1 - - + +
4A GLY* 1.3 67.4 + - - +
5A PRO* 3.4 3.6 - - + -
6A GLU* 3.1 16.9 + - - +
7A LEU* 3.2 14.6 - - - +
54A LYS* 4.4 3.1 - - - +
173A GLY 3.9 7.2 - - - +
175A GLY* 3.1 25.0 + - - -
176A ASN* 3.1 6.5 + - - +
177A TYR* 2.8 53.9 + - + -
178A LEU* 3.0 37.5 + - + +
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Residues in contact with GLY 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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3A GLU* 1.3 69.4 - - - +
5A PRO* 1.3 68.1 - - - +
7A LEU* 3.2 4.3 + - - +
8A HIS* 3.1 21.8 + - - +
53A GLY* 3.7 18.1 + - - +
54A LYS* 4.4 0.4 - - - +
136A CYS* 6.4 0.7 - - - -
137A VAL* 6.0 1.1 - - - -
138A LEU* 3.9 13.2 - - - +
173A GLY* 2.8 27.3 + - - -
233A PRO* 5.9 0.2 - - - -
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Residues in contact with PRO 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU 3.4 4.7 - - - -
4A GLY* 1.3 87.6 - - - +
6A GLU* 1.3 56.0 - - - +
8A HIS* 3.3 1.9 + - - +
9A LEU* 2.9 38.4 + - + +
138A LEU* 3.9 2.0 - - + -
177A TYR* 3.6 17.3 - - - +
178A LEU* 3.9 15.7 - - + -
233A PRO* 3.5 35.2 - - + +
236A VAL* 3.5 28.9 - - + -
237A VAL* 4.0 15.7 - - + +
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Residues in contact with GLU 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 PRO* 3.5 27.3 - - + +
3A GLU 3.1 12.5 + - - +
5A PRO* 1.3 79.3 - - - +
7A LEU* 1.3 59.3 + - + +
9A LEU* 3.2 9.0 + - - +
10A ALA* 2.8 28.8 + - - +
79A PHE* 4.3 14.9 - - + -
83A GLY 4.5 5.2 - - - +
84A SER* 5.8 0.3 - - - -
177A TYR* 5.4 0.2 + - - -
244A TYR* 4.1 25.2 + - + -
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Residues in contact with LEU 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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2A PRO* 3.8 23.6 - - + -
3A GLU 3.2 18.2 - - - +
4A GLY 3.2 2.1 + - - +
6A GLU* 1.3 75.8 - - + +
8A HIS* 1.3 62.9 + - - +
10A ALA* 3.3 5.0 + - - +
11A SER* 3.0 24.3 + - - -
51A ALA* 3.6 12.2 - - + +
53A GLY 3.6 13.5 - - - +
54A LYS* 3.5 41.1 - - + +
55A GLU* 4.2 2.2 - - - +
56A LEU* 4.1 14.4 - - + +
79A PHE* 3.8 39.3 - - + -
2000A TRS 6.1 0.4 - - - +
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Residues in contact with HIS 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 GLY 3.1 12.1 + - - +
5A PRO* 3.5 7.6 - - + +
7A LEU* 1.3 76.1 - - - +
9A LEU* 1.3 68.4 + - + +
11A SER* 3.2 5.2 + - - -
12A GLN* 3.0 35.2 + - + +
51A ALA* 3.9 14.7 - - + +
138A LEU* 4.2 15.7 - - + +
139A GLN* 3.3 29.6 + - - +
237A VAL* 3.4 37.0 - - + +
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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 PRO* 2.9 27.3 + - + +
6A GLU* 3.7 6.7 - - - +
8A HIS* 1.3 80.0 - - + +
10A ALA* 1.3 62.4 + - - +
12A GLN* 3.4 13.3 + - - +
13A PHE* 3.0 21.8 + - - +
236A VAL* 4.3 12.3 - - + +
237A VAL* 3.8 28.5 - - + +
240A GLY* 4.0 21.3 - - - +
241A GLY 3.5 24.9 - - - +
244A TYR* 3.9 21.6 - - + +
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 2.8 21.4 + - - +
7A LEU 3.5 4.9 - - - +
9A LEU* 1.3 69.8 - - - +
11A SER* 1.3 66.0 + - - +
13A PHE* 3.2 4.2 + - - +
14A VAL* 3.0 27.4 + - - +
56A LEU* 3.8 5.8 - - + -
79A PHE* 3.7 24.0 - - + -
85A PHE* 5.2 1.1 - - + -
244A TYR* 3.7 34.2 - - + -
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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
----------------------------------------------------------
7A LEU 3.0 13.8 + - - -
8A HIS* 3.2 9.8 + - - -
10A ALA* 1.3 72.4 - - - +
12A GLN* 1.3 66.8 + - - +
14A VAL* 3.3 2.4 + - - +
15A ASN* 3.1 30.0 + - - -
49A ALA* 3.1 15.7 + - - +
50A SER* 3.1 40.4 - - - -
51A ALA* 3.9 5.4 - - - -
56A LEU* 3.7 11.4 - - - +
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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 HIS* 3.0 28.2 + - + +
9A LEU* 3.5 15.9 + - - +
11A SER* 1.3 77.3 - - - +
13A PHE* 1.3 63.6 + - - +
15A ASN* 3.4 6.5 + - - +
16A GLU* 3.0 27.9 + - + +
237A VAL* 5.8 1.0 - - - +
241A GLY 3.0 27.5 + - - -
242A ARG* 3.5 32.5 - - + +
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Residues in contact with PHE 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 13.3 + - - +
10A ALA 3.2 8.5 + - - +
12A GLN* 1.3 78.2 - - - +
14A VAL* 1.3 65.5 + - + +
16A GLU* 3.9 3.2 - - - +
17A ALA* 2.9 51.4 + - + +
85A PHE* 3.7 26.9 - - + -
86A GLN* 4.4 1.3 - - - -
87A LEU* 3.9 29.8 - - + -
112A LEU* 4.9 6.5 - - + -
244A TYR* 3.4 45.1 - + + +
245A GLY* 3.8 23.6 - - - -
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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
----------------------------------------------------------
10A ALA 3.0 15.7 + - - +
11A SER* 3.3 6.7 + - - +
13A PHE* 1.3 81.6 - - + +
15A ASN* 1.3 58.5 + - - +
17A ALA* 4.7 0.9 - - - -
18A CYS* 2.8 46.4 + - + +
47A ILE* 4.0 15.7 - - + -
48A SER 4.7 2.0 - - - -
49A ALA* 4.0 10.5 - - + -
56A LEU* 4.9 1.6 - - + -
58A LEU* 3.8 26.9 - - + -
85A PHE* 4.3 33.0 - - + -
112A LEU* 4.3 7.9 - - + -
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Residues in contact with ASN 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* 3.1 22.5 + - - +
12A GLN* 3.8 6.2 - - - +
14A VAL* 1.3 80.8 - - - +
16A GLU* 1.3 57.4 + - - +
18A CYS* 5.0 1.6 - - - -
19A ARG* 2.8 32.4 + - - +
47A ILE 5.1 0.8 - - - +
48A SER* 3.3 14.7 - - - +
49A ALA 2.6 47.4 + - - +
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Residues in contact with GLU 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 21.6 + - + +
13A PHE* 4.0 4.0 - - + +
15A ASN* 1.3 77.5 - - - +
17A ALA* 1.3 57.8 + - - +
19A ARG* 3.0 54.8 + - - +
242A ARG* 5.6 8.5 - - - +
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Residues in contact with ALA 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 PHE* 2.9 43.1 + - + +
14A VAL* 4.0 2.2 - - - +
16A GLU* 1.3 77.9 - - - +
18A CYS* 1.3 63.5 + - - +
19A ARG* 5.0 0.3 - - - +
20A ALA 5.0 1.2 + - - -
21A LEU* 3.2 21.1 - - - +
87A LEU* 3.9 19.4 - - + +
112A LEU* 6.4 0.4 - - + -
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Residues in contact with CYS 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* 2.8 25.0 + - - +
15A ASN 3.7 0.4 - - - +
17A ALA* 1.3 83.0 - - - +
19A ARG* 1.3 65.6 + - - +
20A ALA 3.2 2.9 - - - -
21A LEU* 3.0 27.7 + - - +
23A PHE* 3.9 30.9 - - + -
46A ARG* 4.5 1.9 + - - +
47A ILE* 3.5 26.4 + - + +
87A LEU* 5.4 2.0 - - - -
112A LEU* 4.0 25.1 - - - -
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Residues in contact with ARG 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 ASN 2.8 15.2 + - - +
16A GLU* 3.0 45.2 + - - +
17A ALA 4.8 0.9 - - - +
18A CYS* 1.3 77.2 - - - +
20A ALA* 1.3 72.3 + - + +
46A ARG* 3.5 18.9 + - - -
47A ILE 5.5 0.9 - - - -
242A ARG* 5.6 7.5 - - - +
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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