Contacts of the helix formed by residues 18 - 31 (chain C) in PDB entry 1IB1
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 ARG 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA* 2.8 12.4 + - - +
16C ALA* 3.6 16.4 - - - +
17C GLU* 1.3 76.1 - - - +
19C TYR* 1.3 62.6 + - - +
20C ASP* 3.2 3.6 - - - -
21C ASP* 3.1 35.5 + - - +
22C MET 3.2 8.7 + - - -
55D ARG* 4.3 16.2 - - - +
58D SER* 3.7 25.8 + - - +
82D TYR* 3.1 29.0 + - - +
85D LYS* 3.7 8.5 - - - +
86D ILE* 3.9 18.4 - - - +
89D GLU* 3.0 42.0 + - - -
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 3.7 41.2 + - + +
17C GLU* 3.5 37.0 + - - +
18C ARG* 1.3 68.9 - - - +
20C ASP* 1.3 61.3 + - - +
22C MET* 3.5 22.1 - - - +
23C ALA* 2.9 24.4 + - - +
46C VAL* 4.5 2.5 - - + -
47C ALA* 4.1 2.4 - - - +
50C ASN* 3.4 55.8 + - + -
51C VAL* 3.2 18.8 - - + +
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Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 3.2 1.7 + - - -
19C TYR* 1.3 78.5 + - - +
21C ASP* 1.3 64.2 + - - +
23C ALA* 3.6 2.9 + - - +
24C ALA* 3.2 21.5 + - - +
51C VAL* 3.6 17.3 - - - +
55C ARG* 3.1 39.8 + - - -
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Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LYS* 5.0 6.5 - - - -
13C ALA* 3.9 3.6 - - + -
18C ARG* 3.1 36.4 + - - +
20C ASP* 1.3 80.4 - - - +
22C MET* 1.3 65.0 + - - +
24C ALA* 3.1 8.4 + - - +
25C CYS* 3.0 28.8 + - - -
82D TYR* 2.9 33.6 + - + +
85D LYS* 3.7 19.5 + - - -
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Residues in contact with MET 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.4 22.0 - - + +
13C ALA* 3.6 17.6 - - + +
14C GLU* 3.4 44.0 - - + +
18C ARG 3.2 4.3 + - - +
19C TYR* 3.3 29.6 + - - +
21C ASP* 1.3 80.0 - - - +
23C ALA* 1.3 60.9 + - - +
25C CYS* 3.4 3.1 + - - +
26C MET* 3.1 24.1 + - + +
43C LEU* 3.7 35.2 - - + +
46C VAL* 4.1 8.7 - - + -
47C ALA* 3.7 14.1 - - + -
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR 2.9 17.2 + - - +
20C ASP* 3.8 5.4 - - - +
22C MET* 1.3 74.7 - - - +
24C ALA* 1.3 54.9 + - - +
26C MET* 3.2 3.1 + - - +
27C LYS* 2.7 37.0 + - - +
47C ALA* 3.6 17.0 - - + +
48C TYR* 4.0 27.7 + - + +
51C VAL* 4.0 14.8 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ASP 3.2 11.4 + - - +
21C ASP* 3.1 12.2 + - - +
23C ALA* 1.3 79.2 - - - +
25C CYS* 1.3 63.8 + - - +
27C LYS* 3.3 9.8 + - - +
28C SER* 3.1 27.3 + - - -
48C TYR* 5.6 0.2 - - - -
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Residues in contact with CYS 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.4 36.4 - - + +
9C LYS* 3.7 40.2 - - - -
10C ALA* 3.8 12.1 - - + -
21C ASP* 3.0 19.3 + - - -
22C MET 3.5 7.2 - - - +
24C ALA* 1.3 77.6 - - - +
26C MET* 1.3 58.1 + - - +
28C SER* 3.1 6.4 + - - -
29C VAL* 3.1 30.1 + - - +
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Residues in contact with MET 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 4.6 5.2 - - + -
10C ALA* 3.7 22.7 - - + -
22C MET* 3.1 17.0 + - + +
23C ALA* 3.8 4.3 - - - +
25C CYS* 1.3 79.7 - - - +
27C LYS* 1.3 60.0 + - - +
29C VAL* 3.5 23.5 + - + +
30C THR* 2.7 33.8 + - - -
36C LEU* 5.0 2.5 - - + -
40C GLU* 3.3 45.5 - - + +
43C LEU* 3.9 17.3 - - + +
44C LEU* 3.5 37.7 - - + +
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA 2.7 16.9 + - - +
24C ALA* 3.6 10.5 - - - +
25C CYS 3.2 0.2 - - - -
26C MET* 1.3 77.5 - - - +
28C SER* 1.3 63.2 + - - +
30C THR* 3.5 3.0 + - - -
31C GLU* 2.8 61.3 + - - +
44C LEU* 4.3 0.4 - - - +
48C TYR* 3.5 13.7 - - - +
96C ASP* 3.2 34.1 - - - +
100C LEU* 4.0 26.0 - - + -
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LEU* 3.9 19.7 - - - -
24C ALA 3.1 13.7 + - - -
25C CYS* 3.1 9.1 + - - -
27C LYS* 1.3 75.1 - - - +
29C VAL* 1.3 66.1 - - - +
31C GLU* 3.0 23.9 + - - +
32C GLN* 3.4 15.1 + - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 4.1 31.5 - - + +
6C LEU* 3.4 29.8 - - + +
7C VAL* 4.2 7.9 - - + -
25C CYS 3.1 15.7 + - - +
26C MET* 3.9 20.6 - - + +
27C LYS 3.4 0.2 - - - -
28C SER* 1.3 74.3 - - - +
30C THR* 1.3 62.6 + - - +
32C GLN* 3.2 24.2 + - - +
33C GLY 4.5 0.2 + - - -
34C ALA 4.8 2.6 + - - +
36C LEU* 4.0 19.8 - - + +
40C GLU* 4.0 14.1 - - - +
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Residues in contact with THR 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C MET 2.7 22.4 + - - -
27C LYS* 3.7 5.6 - - - -
29C VAL* 1.3 76.6 - - - +
31C GLU* 1.3 57.1 + - - +
32C GLN 3.1 4.7 + - - -
33C GLY* 3.2 13.2 + - - -
34C ALA 4.5 1.8 + - - +
36C LEU* 3.7 27.4 - - + +
44C LEU* 3.9 8.0 - - - +
100C LEU* 4.1 11.2 - - + -
104C PHE* 3.5 32.2 - - + +
105C LEU* 3.7 33.7 - - + -
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LYS* 2.8 58.1 + - - +
28C SER* 3.0 20.0 + - - +
30C THR* 1.3 74.0 - - - +
32C GLN* 1.3 56.0 + - - +
33C GLY 3.0 7.8 + - - -
100C LEU* 4.2 7.6 - - + +
104C PHE* 3.8 31.6 - - + -
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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