Contacts of the helix formed by residues 2 - 18 (chain A) in PDB entry 5T8Y
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 ASN 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 1.3 79.9 + - + +
4A TYR* 3.2 6.2 - - - +
5A GLN* 3.1 28.2 + - - +
6A LEU* 2.9 29.1 + - - +
125A GLU* 5.1 12.6 + - - +
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Residues in contact with VAL 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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2A ASN* 1.3 90.4 - - + +
4A TYR* 1.3 62.9 + - - +
6A LEU* 3.4 5.8 + - - +
7A LYS* 3.1 21.5 + - - +
176A ILE* 4.2 8.5 - - + -
177A PRO* 3.6 40.8 - - + +
178A PHE* 3.7 21.1 - - + -
179A GLU* 5.3 3.4 - - + +
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Residues in contact with TYR 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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2A ASN 3.2 5.1 - - - +
3A VAL* 1.3 80.9 - - - +
5A GLN* 1.3 59.3 + - + +
7A LYS* 3.3 18.0 + - + +
8A GLU* 3.1 66.9 + - + +
179A GLU* 6.5 1.6 - - + -
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Residues in contact with GLN 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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2A ASN* 3.1 27.0 + - - +
4A TYR* 1.3 80.9 - - + +
6A LEU* 1.3 59.7 + - - +
8A GLU* 3.2 8.0 + - - +
9A GLU* 3.0 53.1 + - + +
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Residues in contact with LEU 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 ASN 2.9 15.0 + - - +
3A VAL* 3.4 7.2 + - - +
5A GLN* 1.3 76.4 - - - +
7A LYS* 1.3 57.9 + - - +
9A GLU* 3.5 6.2 + - - +
10A LEU* 2.9 30.1 + - - +
119A PHE* 4.0 26.7 - - + -
120A LEU* 4.0 7.0 - - + -
123A LYS* 4.1 22.0 - - + -
125A GLU* 4.3 11.0 - - - +
127A ILE* 4.1 13.5 - - + -
176A ILE* 3.7 35.4 - - + -
178A PHE* 4.1 8.7 - - + -
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Residues in contact with LYS 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 VAL 3.1 13.2 + - - +
4A TYR* 3.4 21.0 - - + +
5A GLN 3.2 0.2 - - - -
6A LEU* 1.3 78.4 - - - +
8A GLU* 1.3 64.3 + - - +
10A LEU* 3.3 5.3 + - - +
11A ILE* 3.0 44.5 + - + +
24A PHE* 3.5 37.2 - - + -
178A PHE* 3.6 22.4 - - + -
179A GLU* 2.5 41.9 + - + +
180A PRO 4.8 0.4 + - - -
181A ASP* 3.6 14.7 + - - -
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Residues in contact with GLU 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 TYR* 3.1 58.0 + - + +
5A GLN* 3.2 9.4 + - + +
7A LYS* 1.3 81.7 - - - +
9A GLU* 1.3 62.4 + - + +
11A ILE* 3.5 15.6 + - - +
12A GLU* 3.0 32.1 + - - +
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Residues in contact with GLU 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 GLN* 3.0 44.9 + - + +
6A LEU* 3.9 9.3 - - - +
8A GLU* 1.3 76.7 - - + +
10A LEU* 1.3 57.6 + - - +
12A GLU* 3.9 12.8 - - - +
13A TYR* 3.0 31.0 + - - +
119A PHE* 3.8 12.8 - - + -
123A LYS* 2.8 33.9 + - - -
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Residues in contact with LEU 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 LEU 2.9 18.6 + - - +
7A LYS 3.4 4.9 - - - +
8A GLU 3.2 0.2 - - - -
9A GLU* 1.3 74.7 - - - +
11A ILE* 1.3 64.6 + - - +
13A TYR* 3.4 1.8 + - + +
14A ALA* 3.0 26.9 + - - +
22A ILE* 4.4 6.7 - - + -
24A PHE* 3.6 32.1 - - + -
71A VAL* 4.2 12.8 - - + -
116A LEU* 4.1 25.6 - - + +
119A PHE* 3.7 30.3 - - + -
120A LEU* 4.4 12.3 - - + -
172A MET* 5.1 2.9 - - + -
178A PHE* 3.9 19.3 - - + -
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Residues in contact with ILE 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 LYS* 3.0 33.3 + - + +
8A GLU* 3.9 18.4 - - - +
10A LEU* 1.3 75.3 - - - +
12A GLU* 1.3 64.3 + - - +
14A ALA* 3.5 1.6 + - - +
15A LYS* 3.3 39.0 + - + +
22A ILE* 3.9 27.5 - - + +
24A PHE* 3.8 28.9 - - + -
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Residues in contact with GLU 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 GLU 3.0 19.2 + - - +
9A GLU* 3.9 13.5 - - - +
11A ILE* 1.3 80.0 - - - +
13A TYR* 1.3 61.9 + - - +
15A LYS* 3.6 5.8 + - - +
16A SER* 3.5 19.2 + - - -
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Residues in contact with TYR 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 GLU 3.0 20.2 + - - +
10A LEU 3.9 2.2 - - - +
11A ILE 3.3 0.2 - - - -
12A GLU* 1.3 75.1 - - - +
14A ALA* 1.3 66.4 + - - +
16A SER* 2.4 28.7 + - - -
17A ILE* 3.3 30.0 + - + +
115A LEU* 3.8 31.3 + - - +
116A LEU* 4.1 17.9 - - + -
119A PHE* 3.7 44.4 - + + -
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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 LEU 3.0 17.8 + - - +
11A ILE 3.9 3.6 - - - +
13A TYR* 1.3 78.3 - - - +
15A LYS* 1.3 60.0 + - - +
17A ILE* 3.2 17.9 - - - +
19A VAL* 3.0 42.1 + - + +
22A ILE* 4.2 19.7 - - + -
116A LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 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 ILE* 3.3 32.1 + - + +
12A GLU* 4.0 5.6 - - - +
13A TYR 3.2 0.6 - - - -
14A ALA* 1.3 78.6 - - + +
16A SER* 1.3 61.8 + - - +
17A ILE 3.5 0.2 + - - -
18A GLY* 3.7 8.2 + - - -
19A VAL* 3.5 16.5 + - + +
20A ASP* 3.1 27.9 + - - +
21A LYS* 4.4 5.1 - - - +
22A ILE* 5.1 9.4 - - + -
163A TYR* 5.3 0.4 + - - -
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Residues in contact with SER 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 GLU 3.5 9.2 + - - -
13A TYR* 2.4 40.6 + - - -
15A LYS* 1.3 79.8 - - - +
17A ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 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 TYR* 3.4 38.8 - - + +
14A ALA* 3.2 14.6 - - - +
16A SER* 1.3 83.0 - - - +
18A GLY* 1.3 52.7 + - - +
19A VAL* 4.5 2.7 - - + +
112A LYS* 2.4 59.7 + - + +
115A LEU* 4.1 24.0 - - + -
116A LEU* 3.6 29.8 - - + -
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Residues in contact with GLY 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 3.4 0.8 + - - -
15A LYS 3.7 5.8 + - - -
16A SER 3.5 3.0 - - - -
17A ILE* 1.3 81.1 - - - +
19A VAL* 1.3 66.9 + - - +
20A ASP* 3.2 7.8 + - - +
75A LEU* 4.4 3.5 - - - +
112A LYS* 4.2 7.4 - - - -
258A HIS* 3.1 34.4 + - - -
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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