Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 5HLX
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 SER 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 LEU* 1.3 76.8 - - - +
4A GLU* 1.3 65.6 + - - +
5A GLY* 3.5 4.9 + - - -
6A GLU* 2.8 40.6 + - - +
7A TRP* 3.0 22.7 + - - -
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Residues in contact with GLU 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 SER* 1.3 72.9 - - - +
5A GLY* 1.3 57.4 + - - +
7A TRP* 3.3 6.1 + - - +
8A GLN* 2.9 59.4 + - - +
79A LYS* 3.5 30.6 + - - -
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Residues in contact with GLY 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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3A SER* 3.2 6.5 + - - -
4A GLU* 1.3 77.7 - - - +
6A GLU* 1.3 62.4 + - - +
8A GLN* 3.3 12.0 + - - +
9A LEU* 3.0 29.0 + - - +
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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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1A VAL 4.4 0.5 - - - +
2A LEU* 3.3 17.1 - - + +
3A SER* 2.8 45.6 + - - +
5A GLY* 1.3 77.2 - - - +
7A TRP* 1.3 62.5 + - - +
9A LEU* 3.1 7.3 + - + -
10A VAL* 3.0 25.5 + - - +
126A ASP 5.6 0.7 - - - +
129A GLY 5.7 0.2 - - - -
130A ALA* 3.4 25.6 + - + +
133A LYS* 2.6 41.4 + - - -
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Residues in contact with TRP 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 LEU* 3.4 42.2 + - + +
3A SER 3.0 26.1 + - - -
4A GLU* 3.6 10.1 - - - +
6A GLU* 1.3 76.0 - - - +
8A GLN* 1.3 56.6 + - - +
10A VAL* 3.2 13.8 + - + +
11A LEU* 2.9 33.1 + - + +
75A ILE 5.7 0.2 - - - -
76A LEU* 3.7 29.8 - - + -
79A LYS* 3.0 64.8 + - + +
80A GLY* 3.3 17.5 - - - -
82A HIS* 5.7 2.5 - + - -
134A ALA* 3.9 28.5 - - + -
137A LEU* 4.1 9.9 - - + -
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Residues in contact with GLN 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 GLU* 2.9 51.2 + - - +
5A GLY* 3.6 12.1 - - - +
6A GLU 3.2 0.2 - - - -
7A TRP* 1.3 74.5 - - - +
9A LEU* 1.3 59.2 + - + +
11A LEU* 3.8 5.5 - - - +
12A HIS* 2.9 31.2 + - - +
79A LYS* 5.5 2.0 - - - +
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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 GLY 3.0 20.2 + - - +
6A GLU* 3.1 10.3 + - + +
8A GLN* 1.3 74.1 - - + +
10A VAL* 1.3 67.2 + - - +
12A HIS* 3.4 10.8 + - + +
13A VAL* 3.2 24.0 + - - +
122A ASP 5.0 0.5 - - - +
126A ASP* 3.7 52.3 - - + +
127A ALA* 4.1 21.1 - - + +
130A ALA* 4.3 5.6 - - + -
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Residues in contact with VAL 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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2A LEU* 4.4 3.6 - - + -
6A GLU 3.0 15.9 + - - +
7A TRP* 3.4 15.3 - - + +
9A LEU* 1.3 78.2 - - - +
11A LEU* 1.3 62.6 + - + +
13A VAL* 3.4 5.2 - - - +
14A TRP* 2.9 25.8 + - - +
76A LEU* 4.1 33.2 - - + -
127A ALA 5.7 0.9 - - - -
130A ALA* 3.7 31.9 - - + +
131A MET* 3.8 27.7 - - + +
134A ALA* 4.1 7.4 - - + -
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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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7A TRP* 2.9 18.7 + - + +
8A GLN* 4.1 4.5 - - - +
10A VAL* 1.3 78.6 - - + +
12A HIS* 1.4 64.8 + - - +
14A TRP* 3.7 9.1 - - + +
15A ALA* 3.0 23.2 + - - +
18A GLU* 5.1 1.2 - - - +
76A LEU* 3.9 26.2 - - + +
77A LYS* 3.9 38.8 - - + +
79A LYS* 3.6 30.7 - - + +
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Residues in contact with HIS 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 GLN 2.9 18.4 + - - +
9A LEU* 3.7 13.5 - - + +
10A VAL 3.3 0.2 - - - -
11A LEU* 1.4 77.5 - - - +
13A VAL* 1.3 63.2 + - - +
15A ALA* 3.3 18.1 + - - +
16A LYS* 3.8 11.6 + - + +
122A ASP* 3.0 39.1 + - + -
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Residues in contact with VAL 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 3.2 10.1 + - - +
10A VAL* 3.4 11.4 - - - +
12A HIS* 1.3 79.4 - - - +
14A TRP* 1.3 69.4 + - - +
16A LYS* 3.0 25.5 + - + +
17A VAL* 3.4 5.9 + - - +
115A LEU* 4.3 15.7 - - + -
119A HIS* 4.1 26.5 - - + -
122A ASP* 3.6 24.7 - - + +
123A PHE* 4.1 22.0 - - + -
127A ALA* 5.3 1.6 - - + +
131A MET* 3.8 20.2 - - + -
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Residues in contact with TRP 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 VAL 2.9 18.3 + - - +
11A LEU* 3.8 15.5 - - + +
12A HIS 3.2 0.4 - - - -
13A VAL* 1.3 78.1 - - - +
15A ALA* 1.3 63.4 + - - +
17A VAL* 3.0 38.3 + - + +
18A GLU* 3.0 36.7 + - + +
28A ILE* 5.7 0.9 - - + -
69A LEU* 3.8 40.3 + - + -
72A LEU* 3.8 22.2 - - + -
73A GLY* 3.4 28.8 - - - -
76A LEU* 3.6 22.2 - - + -
77A LYS* 4.8 5.6 - - - -
111A ILE* 4.4 16.8 - - + -
115A LEU* 4.5 3.6 - - + -
131A MET* 4.1 17.3 - - + -
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Residues in contact with ALA 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 13.1 + - - +
12A HIS* 3.5 12.8 - - - +
13A VAL 3.1 0.6 - - - -
14A TRP* 1.3 75.1 - - - +
16A LYS* 1.3 63.1 + - + +
18A GLU* 3.2 26.4 + - - +
19A ALA* 3.4 10.9 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 3.9 13.2 - - + +
13A VAL* 3.0 16.6 + - + +
15A ALA* 1.3 78.0 - - + +
17A VAL* 1.3 65.1 + - - +
19A ALA* 3.3 18.4 + - - +
24A HIS* 3.6 11.4 - - - -
119A HIS* 3.6 39.9 + - + +
122A ASP* 3.1 28.6 + - - +
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Residues in contact with VAL 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 VAL 3.9 8.1 - - - +
14A TRP* 3.0 41.8 + - + +
16A LYS* 1.3 75.8 - - - +
18A GLU* 1.3 57.8 + - - +
20A ASP 3.0 31.2 + - - +
21A VAL* 3.3 5.9 + - + -
24A HIS* 3.6 31.8 + - + +
28A ILE* 5.8 1.8 - - + -
69A LEU* 4.0 18.2 - - + -
115A LEU* 3.4 33.2 - - + -
119A HIS* 5.1 0.2 - - - +
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Residues in contact with GLU 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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11A LEU 5.1 0.9 - - - +
14A TRP* 3.0 29.5 + - + +
15A ALA* 3.6 25.9 + - - +
16A LYS 3.2 0.6 - - - -
17A VAL* 1.3 76.7 - - - +
19A ALA* 1.3 61.2 + - - +
20A ASP 3.2 0.8 + - - -
21A VAL* 3.8 21.4 + - + +
77A LYS* 2.8 39.2 + - - -
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Residues in contact with ALA 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 ALA 3.4 8.4 + - - +
16A LYS* 3.3 15.3 + - - +
17A VAL 3.2 1.0 + - - -
18A GLU* 1.3 76.8 - - - +
20A ASP* 1.3 61.2 + - + +
24A HIS* 6.0 0.2 - - + -
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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