Contacts of the helix formed by residues 14 - 22 (chain D) in PDB entry 4OIP
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 14 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 3.9 3.6 + - - -
13D ALA* 1.3 74.5 - - - +
15D PRO* 1.3 66.1 - - - +
16D GLU* 3.3 20.2 + - - +
17D LYS* 2.9 27.5 + - - +
18D ILE* 2.9 26.6 + - - +
511D TRP* 3.4 38.8 - - - -
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Residues in contact with PRO 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA 4.3 2.5 - - - +
14D SER* 1.3 85.8 - - - +
16D GLU* 1.3 66.1 + - - +
18D ILE* 3.3 14.4 + - + +
19D ARG* 2.9 55.1 + - - +
462D GLN* 5.6 1.3 - - - +
510D GLU 5.9 0.2 - - - +
511D TRP* 4.2 18.4 - - + -
513D ILE 4.8 5.8 - - - +
514D LEU* 5.5 2.9 - - + -
515D GLU* 3.7 41.1 - - + +
516D ALA* 4.6 5.7 - - + +
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 3.3 22.3 + - - +
15D PRO* 1.3 88.6 - - - +
17D LYS* 1.3 61.0 + - - +
19D ARG* 3.5 18.4 + - - +
20D SER* 2.9 27.9 + - - -
511D TRP* 4.7 5.9 + - - -
515D GLU* 4.9 2.8 - - - +
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C ASP* 4.1 18.0 + - + +
1100C GLN* 4.4 10.7 - - - +
12D LEU 6.0 0.7 - - - -
13D ALA* 4.1 11.2 - - + +
14D SER* 2.9 30.3 + - - +
16D GLU* 1.3 78.1 - - - +
18D ILE* 1.3 57.7 + - - +
20D SER* 2.3 28.9 + - - +
21D TRP* 2.9 51.5 + - + +
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096C ALA* 4.0 7.0 - - + -
13D ALA* 4.0 17.0 - - + +
14D SER 2.9 17.5 + - - +
15D PRO* 3.3 11.4 + - + +
17D LYS* 1.3 76.8 - - - +
19D ARG* 1.3 56.1 + - - +
21D TRP* 3.2 15.7 + - + +
22D SER* 3.0 25.8 + - - -
91D GLY 5.1 1.0 - - - +
92D HIS* 4.4 9.2 - - + -
514D LEU* 3.6 21.5 - - + -
516D ALA* 3.3 31.0 - - + +
518D PRO* 3.7 40.8 - - + -
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Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118C LYS* 3.6 6.6 + - - -
15D PRO* 2.9 43.9 + - - +
16D GLU* 3.6 20.1 + - - +
18D ILE* 1.3 75.5 - - - +
20D SER* 1.3 61.1 + - - +
22D SER* 3.3 26.4 + - - +
92D HIS* 4.8 10.7 - - + +
94D GLU* 2.7 44.2 + - - +
515D GLU* 3.4 27.5 + - - +
516D ALA* 4.4 7.8 - - + +
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118C LYS* 3.2 27.1 + - - +
16D GLU 2.9 15.5 + - - -
17D LYS* 2.3 34.3 + - - +
19D ARG* 1.3 75.6 - - - +
21D TRP* 1.3 69.3 + - - +
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Residues in contact with TRP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LYS* 5.9 0.9 - - - +
1093C GLN* 3.7 51.5 - - + +
1096C ALA* 4.8 0.4 - - - -
1097C LEU 3.7 5.6 - - - -
1098C ASP* 3.2 44.5 + - + -
1100C GLN* 5.7 1.6 - - - +
1116C ALA 4.5 8.0 - - - +
13D ALA* 3.6 26.2 - - + -
17D LYS* 2.9 34.9 + - + +
18D ILE* 3.4 24.2 - - + +
20D SER* 1.3 86.0 + - - +
22D SER* 1.3 63.1 + - - +
23D TYR* 3.5 19.2 + - - -
90D MET* 3.9 26.2 + - + +
518D PRO* 5.1 0.2 - - + -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118C LYS* 3.1 27.2 + - - +
18D ILE 3.0 15.8 + - - -
19D ARG 3.3 8.2 + - - +
21D TRP* 1.3 76.9 - - - +
23D TYR* 1.3 58.7 + - - +
24D GLY 2.6 32.1 + - - -
90D MET 3.2 9.2 - - - -
91D GLY 3.1 10.3 - - - -
92D HIS* 2.7 27.9 + - - -
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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