Contacts of the helix formed by residues 12 - 23 (chain B) in PDB entry 1IVS
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 VAL 12 (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* 6.3 0.7 - - - -
7B TYR* 3.7 36.3 - - + +
9B PRO 2.7 3.3 + - - +
11B SER* 1.3 95.6 - - - +
13B GLU* 1.3 63.1 + - - +
14B PRO* 3.6 0.7 - - - -
15B LYS* 3.3 9.4 - - - +
16B TRP* 2.9 32.2 - - + -
685B PHE 4.3 8.1 - - - +
686B LEU* 4.4 1.6 - - - -
689B GLU* 3.3 49.4 - - + +
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Residues in contact with GLU 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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7B TYR* 4.3 2.7 - - - +
9B PRO* 2.8 34.5 + - + +
12B VAL* 1.3 70.7 - - - +
14B PRO* 1.3 70.8 - - + +
15B LYS 3.2 0.3 + - - -
16B TRP 3.2 1.7 + - - -
17B ALA* 2.8 25.7 + - - +
131B ARG* 2.8 30.1 + - - +
547B GLY* 3.7 4.3 - - - -
548B ALA* 3.0 25.7 + - - +
549B ASP* 3.0 38.8 + - - +
685B PHE* 3.1 33.4 - - + -
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Residues in contact with PRO 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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9B PRO 3.3 12.3 - - - +
10B LYS* 4.0 19.1 - - + +
11B SER* 5.1 1.3 - - - -
12B VAL 3.6 7.2 - - - +
13B GLU* 1.3 94.3 - - + +
15B LYS* 1.3 62.9 + - - +
17B ALA* 3.3 6.3 - - + +
18B GLU* 3.2 22.3 + - - +
131B ARG* 4.3 19.5 - - - +
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Residues in contact with LYS 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 SER 4.0 17.0 - - - +
12B VAL* 3.3 11.0 - - - +
14B PRO* 1.3 79.3 - - - +
16B TRP* 1.3 89.0 + - + +
17B ALA 3.1 0.3 + - - -
18B GLU* 3.3 11.1 + - - +
19B LYS* 2.9 23.5 + - - +
689B GLU* 3.0 33.5 + - - -
692B GLN* 5.3 3.8 + - - -
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Residues in contact with TRP 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 VAL* 2.9 32.5 - - + +
13B GLU 3.2 2.8 + - - +
15B LYS* 1.3 102.8 - - + +
17B ALA* 1.3 65.2 + - - +
19B LYS* 3.5 19.0 - - + +
20B TRP* 3.2 49.3 + + + -
685B PHE* 4.2 14.8 - - + -
688B SER* 3.5 31.6 - - - -
689B GLU* 3.5 35.4 - - + +
692B GLN* 3.9 22.9 - - + -
698B GLU 3.2 31.0 - - - -
699B GLU* 3.6 10.5 - - - -
700B LEU 5.6 0.2 - - - -
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Residues in contact with ALA 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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13B GLU 2.8 18.8 + - - +
14B PRO* 3.3 7.0 - - + +
16B TRP* 1.3 79.4 - - - +
18B GLU* 1.3 58.8 + - - +
20B TRP* 3.2 9.1 + - - +
21B ALA* 2.9 25.2 + - - +
130B LYS* 4.5 7.3 - - + +
131B ARG* 4.2 25.4 - - - +
685B PHE* 3.7 19.2 - - + -
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Residues in contact with GLU 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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14B PRO 3.2 10.4 + - - +
15B LYS* 3.6 12.8 - - - +
17B ALA* 1.3 77.1 - - - +
19B LYS* 1.3 70.8 + - - +
21B ALA* 3.5 11.4 - - + -
22B LYS* 2.9 56.6 + - + +
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Residues in contact with LYS 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 LYS 2.9 17.4 + - - +
16B TRP* 3.5 23.6 - - + +
18B GLU* 1.3 83.3 - - + +
20B TRP* 1.3 65.9 + - + +
22B LYS* 3.2 4.4 + - - +
23B ASN* 3.1 32.1 + - + +
692B GLN* 5.4 0.6 - - - +
698B GLU* 3.1 33.7 + - - +
699B GLU* 2.9 31.7 + - - +
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Residues in contact with TRP 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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16B TRP* 3.2 34.6 + + + -
17B ALA* 3.8 6.7 - - - +
19B LYS* 1.3 80.6 - - + +
21B ALA* 1.3 63.7 + - - +
23B ASN* 3.5 7.6 - - - +
24B PRO* 3.3 21.5 - - - +
25B PHE* 3.6 30.2 - + + -
65B ARG* 3.5 36.8 - - - +
130B LYS 5.5 0.2 - - - -
133B GLY* 4.1 8.5 - - - -
134B ALA 5.4 7.9 - - - +
135B SER* 6.0 0.9 - - - -
138B TRP* 4.4 6.0 + - - -
680B HIS* 4.8 0.2 - - - -
684B PRO* 3.9 21.3 - - + -
685B PHE* 3.9 33.4 - + - -
688B SER* 3.7 19.3 - - - -
699B GLU* 3.1 29.1 + - - -
701B ALA* 5.1 0.6 - - + +
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Residues in contact with ALA 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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17B ALA 2.9 14.6 + - - +
18B GLU* 3.3 17.3 - - + +
19B LYS 3.0 0.4 - - - -
20B TRP* 1.3 81.7 - - - +
22B LYS* 1.3 64.3 + - + +
23B ASN 3.3 0.3 + - - -
24B PRO* 3.4 9.7 - - - +
130B LYS* 4.2 40.5 - - + +
138B TRP* 4.4 3.9 - - - +
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Residues in contact with LYS 22 (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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18B GLU* 2.9 44.7 + - + +
19B LYS* 5.2 2.7 - - - +
21B ALA* 1.3 78.1 - - + +
23B ASN* 1.3 75.1 + - - +
24B PRO* 3.4 5.1 - - - +
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Residues in contact with ASN 23 (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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19B LYS* 3.1 21.3 + - + +
20B TRP* 3.5 7.3 - - - +
21B ALA 3.2 0.4 - - - -
22B LYS* 1.3 114.2 + - - +
24B PRO* 1.3 71.4 - - - +
25B PHE* 3.7 7.1 + - - -
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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