Contacts of the helix formed by residues 2 - 16 (chain B) in PDB entry 5AYR
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 THR 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 74.8 - - - +
3B LEU* 1.3 65.5 + - - +
4B GLU* 4.0 11.7 + - - +
5B LEU* 3.0 31.6 + - - +
6B GLN* 3.0 21.7 + - - +
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Residues in contact with LEU 3 (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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2B THR* 1.3 70.1 - - - +
4B GLU* 1.3 58.2 + - - +
6B GLN* 2.7 42.0 + - - +
7B LEU* 3.0 12.3 + - + +
70B ILE* 4.3 13.9 - - + -
72B TYR* 4.2 16.6 - - - +
77B LEU* 3.9 30.1 - - + -
80B ILE* 3.9 26.9 - - + -
105B ARG* 5.8 2.0 - - - -
108B LEU* 4.1 17.7 - - + -
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Residues in contact with GLU 4 (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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2B THR* 4.0 12.9 + - - +
3B LEU* 1.3 76.2 - - - +
5B LEU* 1.3 62.5 + - + +
7B LEU* 3.2 5.3 + - - +
8B LYS* 3.1 27.2 + - - +
23B TRP* 5.2 3.1 - - + -
25B CYS* 5.6 1.4 - - - +
56B TYR* 3.1 41.3 + - + +
70B ILE* 4.2 14.3 - - + +
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Residues in contact with LEU 5 (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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1B MET* 3.3 32.2 - - + +
2B THR* 3.0 26.4 + - - +
4B GLU* 1.3 81.3 - - + +
6B GLN* 1.3 64.7 + - - +
8B LYS* 3.7 15.2 - - + +
9B HIS* 3.2 21.3 + - - +
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Residues in contact with GLN 6 (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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1B MET* 2.6 45.9 + - + +
2B THR 3.0 18.5 + - - +
3B LEU* 2.7 25.7 + - + +
5B LEU* 1.3 74.2 - - - +
7B LEU* 1.3 63.6 + - - +
9B HIS* 3.5 6.2 + - - +
10B TYR* 3.2 17.3 + - - +
108B LEU* 3.7 46.5 - - + +
109B THR* 5.5 4.1 - - + +
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Residues in contact with LEU 7 (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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3B LEU* 3.0 12.3 + - + +
4B GLU* 3.7 7.9 - - - +
5B LEU 3.2 0.2 - - - -
6B GLN* 1.3 74.6 - - - +
8B LYS* 1.3 56.1 + - - +
10B TYR* 3.3 2.0 + - + +
11B ILE* 2.8 57.1 + - + +
23B TRP* 5.1 2.2 - - + -
56B TYR* 4.6 8.1 - - + -
68B PRO* 3.8 20.9 - - + -
69B PHE 4.0 9.2 - - - +
70B ILE* 4.0 28.7 - - + -
80B ILE* 3.8 20.9 - - + -
81B GLY 4.3 9.0 - - - +
82B TYR* 5.9 0.2 - - + -
92B LEU* 4.3 17.5 - - + -
108B LEU* 3.8 9.9 - - + -
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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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4B GLU 3.1 16.2 + - - +
5B LEU* 3.7 18.2 - - + +
7B LEU* 1.3 74.6 - - - +
9B HIS* 1.3 63.0 + - - +
11B ILE* 3.8 0.3 - - - +
12B THR* 2.8 43.5 + - + +
18B PRO 4.7 0.7 - - - -
19B LYS 3.3 24.2 + - - +
20B ASP* 4.2 3.4 - - - +
21B GLU 2.5 30.6 + - - -
22B LYS* 4.6 0.6 - - - +
23B TRP* 3.5 54.7 - - + +
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Residues in contact with HIS 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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1B MET* 5.6 8.6 - - - -
5B LEU 3.2 14.8 + - - +
6B GLN* 3.8 7.4 - - - +
7B LEU 3.3 0.4 - - - -
8B LYS* 1.3 82.3 - - - +
10B TYR* 1.3 61.0 + - - +
12B THR* 2.9 22.5 + - - -
13B ASN* 3.0 49.9 + - - -
19B LYS* 6.0 7.0 - - + -
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Residues in contact with TYR 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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6B GLN 3.2 11.3 + - - +
7B LEU* 3.6 5.8 - - + +
9B HIS* 1.3 77.9 - - - +
11B ILE* 1.3 69.3 + - + +
13B ASN* 3.3 8.5 + - + +
14B LEU* 2.7 69.3 + - + +
82B TYR* 4.5 6.1 + + - -
92B LEU* 3.5 36.2 - - + +
107B LEU* 3.8 48.7 - - + +
108B LEU* 3.9 12.1 - - + -
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Residues in contact with ILE 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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7B LEU* 2.8 39.3 + - + +
10B TYR* 1.3 83.0 - - + +
12B THR* 1.3 57.7 + - - +
14B LEU* 4.5 1.3 - - - -
15B PHE* 3.0 45.8 + - + +
17B LEU* 4.3 5.1 - - + +
23B TRP* 3.6 26.7 - - + -
61B LEU* 4.2 12.1 - - + -
66B ILE* 4.5 1.8 - - + -
68B PRO* 4.1 15.9 - - + -
82B TYR* 3.8 39.0 - - + -
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Residues in contact with THR 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* 2.8 36.7 + - + +
9B HIS* 2.9 24.1 + - - -
11B ILE* 1.3 72.2 - - - +
13B ASN* 1.3 65.0 + - - +
16B ASN* 3.0 9.9 + - - -
17B LEU* 3.0 45.6 + - + +
18B PRO 3.9 19.1 - - - +
19B LYS* 4.6 11.9 - - - +
23B TRP* 4.1 18.2 - - + +
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Residues in contact with ASN 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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9B HIS* 3.0 46.7 + - - +
10B TYR* 3.7 7.1 - - + +
12B THR* 1.3 81.5 + - - +
14B LEU* 1.3 69.6 + - - +
15B PHE 3.1 0.9 + - - -
16B ASN* 3.4 6.6 + - - +
19B LYS* 5.6 3.6 + - - +
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Residues in contact with LEU 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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10B TYR* 2.7 58.5 + - + +
11B ILE* 4.5 0.7 - - + -
13B ASN* 1.3 73.6 - - - +
15B PHE* 1.3 91.9 + - + +
16B ASN* 3.8 0.7 + - - +
82B TYR* 3.6 18.4 - - + +
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Residues in contact with PHE 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 ILE* 3.0 27.3 + - + +
14B LEU* 1.3 106.5 - - + +
16B ASN* 1.3 71.8 + - - +
17B LEU* 3.3 23.9 + - + +
64B SER* 6.0 2.2 - - - +
66B ILE* 3.6 46.9 - - + -
82B TYR* 3.8 26.0 - + - -
85B GLU* 4.3 11.4 - - - -
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Residues in contact with ASN 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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12B THR 3.0 9.1 + - - -
13B ASN 3.4 7.3 + - - +
14B LEU 3.5 0.8 + - - +
15B PHE* 1.3 80.0 - - - +
17B LEU* 1.3 65.1 + - - +
18B PRO* 4.7 1.2 - - - +
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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