Contacts of the helix formed by residues 7 - 21 (chain B) in PDB entry 5HOO
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 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B VAL 4.0 1.0 + - - -
6B PRO* 1.3 71.5 - - - +
8B LYS* 1.3 61.3 + - - +
9B GLU* 2.9 23.3 + - - +
10B GLN* 2.6 57.7 + - - +
11B THR* 2.7 31.6 + - - -
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 1.3 78.2 - - - +
9B GLU* 1.3 70.4 + - - +
11B THR* 3.4 10.0 + - - +
12B ARG* 3.0 51.1 + - - +
41B PRO* 4.0 25.9 - - - +
21E T 3.5 34.4 + - - +
40F C 4.8 13.5 - - - +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 2.9 28.4 + - - +
8B LYS* 1.3 84.8 + - - +
10B GLN* 1.3 59.2 + - + +
12B ARG* 3.1 11.6 + - - +
13B THR* 3.0 31.3 + - - +
60B VAL* 3.6 27.0 - - + +
61B ASP* 4.3 15.8 - - - +
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR* 3.4 36.7 + - + +
16A ILE* 4.6 2.8 - - - +
58A PHE 5.2 2.0 + - - -
60A VAL* 4.6 12.5 - - - +
4B PHE* 3.7 27.5 - - + -
5B VAL 4.5 0.7 - - - +
6B PRO* 3.5 14.5 - - + +
7B ASN* 2.6 51.8 + - - +
9B GLU* 1.3 74.1 - - + +
11B THR* 1.3 61.6 + - - +
13B THR* 3.5 3.8 + - - -
14B VAL* 3.2 27.5 + - - +
36B PHE* 6.4 0.2 - - - -
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Residues in contact with THR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 3.9 18.6 + - - +
7B ASN 2.7 23.0 + - - -
8B LYS* 3.5 12.2 + - - +
10B GLN* 1.3 78.3 - - - +
12B ARG* 1.3 63.3 + - + +
14B VAL* 3.3 9.7 + - - +
15B LEU* 3.2 26.5 + - + +
32B LEU* 4.5 20.6 - - + +
36B PHE* 5.9 1.6 - - - -
40B VAL* 5.5 2.5 - - + +
41B PRO* 4.0 32.8 - - + +
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 3.0 45.9 + - - +
9B GLU* 3.1 13.4 + - - +
11B THR* 1.3 75.7 - - + +
13B THR* 1.3 64.5 - - - +
15B LEU* 3.3 14.0 + - + +
16B ILE* 3.2 24.3 + - - +
49B TRP* 3.1 43.6 - - + +
53B PHE* 4.0 2.1 - - + -
60B VAL* 3.2 42.3 + - + +
61B ASP* 4.7 0.8 - - - +
62B ASP* 2.7 32.1 + - - +
20E A 3.3 10.5 + - - -
21E T 3.1 25.7 + - - -
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 6.3 0.9 - - + -
10A GLN* 3.4 62.5 + - + +
13A THR* 4.4 5.6 - - + -
14A VAL* 4.1 9.4 - - + -
36A PHE* 5.7 1.9 - - + -
9B GLU* 3.0 14.8 + - - +
10B GLN* 3.6 11.8 - - - -
12B ARG* 1.3 73.6 - - - +
14B VAL* 1.3 59.5 + - - +
16B ILE* 3.0 15.9 + - + +
17B PHE* 2.9 24.9 + - - +
60B VAL* 4.2 5.8 - - - +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR* 4.1 13.9 - - + -
14A VAL* 4.8 5.4 - - + -
17A PHE* 3.5 62.8 - - + -
10B GLN 3.2 14.2 + - - +
11B THR 3.3 8.7 + - - +
13B THR* 1.3 76.0 - - - +
15B LEU* 1.3 58.2 + - + +
17B PHE* 3.1 8.7 + - + +
18B CYS* 2.8 31.6 + - - -
32B LEU* 3.9 14.6 - - + -
36B PHE* 4.9 7.9 - - + -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.2 23.0 + - + +
12B ARG* 3.5 14.1 - - + +
13B THR 3.2 0.4 - - - -
14B VAL* 1.3 74.7 - - + +
16B ILE* 1.3 64.8 + - - +
18B CYS* 3.9 2.9 - - - +
19B PHE* 3.0 25.1 + - - +
28B SER* 4.5 11.4 - - - -
32B LEU* 4.2 14.8 - - + -
41B PRO* 6.2 1.3 - - + -
46B CYS* 3.8 37.9 - - + +
49B TRP* 4.1 31.9 - - + -
50B PHE* 3.8 15.8 - - + -
53B PHE* 3.7 13.8 - - + -
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 3.4 37.7 - - + -
10A GLN* 4.6 2.9 - - - +
36A PHE* 4.5 2.7 - - + -
12B ARG 3.2 6.9 + - - +
13B THR* 3.0 13.8 + - + +
15B LEU* 1.3 74.8 - - - +
17B PHE* 1.3 63.0 + - - +
19B PHE* 3.4 3.5 + - - +
20B HIS* 2.9 45.9 + - + +
53B PHE* 3.4 32.1 - - + -
58B PHE* 4.0 24.2 - - + +
60B VAL* 3.8 28.7 - - + -
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Residues in contact with PHE 17 (chain B).
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* 3.4 40.8 - - + -
17A PHE* 4.2 21.5 - + - -
18A CYS* 4.3 7.2 - - - -
31A MET* 3.9 36.6 - - + -
32A LEU* 4.2 7.0 - - + -
35A ALA* 3.8 18.2 - - + -
36A PHE* 3.7 30.7 - + + -
13B THR 2.9 11.6 + - - +
14B VAL* 3.2 8.7 - - - +
16B ILE* 1.3 78.2 - - - +
18B CYS* 1.3 63.9 + - - +
20B HIS* 3.2 2.4 + - - +
21B LEU* 3.0 46.9 + - + +
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Residues in contact with CYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 4.2 5.4 - - - -
14B VAL* 2.8 35.6 + - - +
15B LEU* 3.9 5.4 - - - +
17B PHE* 1.3 73.7 - - - +
19B PHE* 1.3 63.2 + - - +
21B LEU* 3.0 19.4 + - - +
23B LYS* 3.1 26.5 + - + +
28B SER* 3.4 39.0 - - - +
31B MET* 4.0 25.6 - - - -
32B LEU* 6.1 0.9 - - - -
50B PHE* 4.6 0.7 - - + -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU 3.0 19.1 + - - +
16B ILE 3.4 4.3 - - - +
18B CYS* 1.3 76.5 - - - +
20B HIS* 1.3 64.0 + + - +
22B LYS* 2.9 24.3 + - - +
23B LYS 4.0 3.3 + - - +
50B PHE* 3.9 39.6 - + + -
53B PHE* 3.2 43.1 - + + -
54B LYS* 3.8 37.0 - - + -
58B PHE* 4.3 13.9 - + - -
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Residues in contact with HIS 20 (chain B).
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 5.2 4.9 + - - -
4A PHE* 3.6 30.3 + + + +
34A GLU 4.0 3.8 - - - +
35A ALA* 3.8 41.7 - - + +
36A PHE* 4.0 10.6 - + + -
16B ILE* 2.9 48.8 + - + +
17B PHE 3.7 4.0 - - - +
19B PHE* 1.3 75.8 - + - +
21B LEU* 1.3 57.0 + - - +
22B LYS* 3.1 28.5 + - - +
58B PHE* 3.8 21.9 - + - -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A MET* 3.3 44.0 - - + +
34A GLU* 3.9 17.6 - - + +
35A ALA* 3.8 15.5 - - + +
17B PHE* 3.0 44.3 + - + +
18B CYS* 3.0 14.1 + - - +
20B HIS* 1.3 73.6 - - - +
22B LYS* 1.3 70.3 + - - +
23B LYS* 3.1 21.7 + - + +
31B MET* 5.4 7.2 - - + -
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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