Contacts of the strand formed by residues 17 - 22 (chain A) in PDB entry 1INL
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 LEU 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ARG 5.1 1.2 + - - -
16A HIS* 1.3 105.5 + - + +
18A TRP* 1.3 69.2 + - - +
33A LYS* 3.6 4.0 - - - +
34A MET* 3.0 49.4 + - + +
35A ASN 4.6 1.8 - - - +
36A ARG* 5.3 2.5 - - - +
37A VAL* 5.9 1.3 - - + -
18B TRP 3.6 0.9 - - - -
19B TYR* 4.2 7.2 - - + -
34B MET* 3.8 30.1 - - + -
37B VAL* 5.3 8.1 - - + -
40B SER* 4.7 4.3 - - - +
47B ARG* 3.5 28.3 - - - +
49B ASP* 3.7 14.6 - - + +
51B PHE* 5.3 1.8 - - + -
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Residues in contact with TRP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLN* 2.8 44.0 + - + -
16A HIS 3.8 8.9 - - - -
17A LEU* 1.3 79.5 - - - +
19A TYR* 1.3 59.9 + - - +
20A PHE* 3.6 23.1 - + + -
31A PHE* 3.7 30.1 - + - -
32A MET 3.5 21.5 - - - -
33A LYS* 3.6 35.2 - - + -
34A MET* 3.5 9.9 - - - +
16B HIS 3.6 0.5 - - - +
17B LEU* 3.5 3.8 - - - -
18B TRP* 2.9 39.9 + - + +
20B PHE* 3.7 30.4 - + - -
22B TYR* 4.9 4.0 + - - -
22D TYR* 4.1 23.6 - + - -
26D ASN 4.3 4.3 - - - -
27D ASN 4.6 2.9 - - - -
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 1.3 74.4 - - - +
20A PHE* 1.3 61.3 + - - +
21A GLU* 3.7 18.9 - - + +
30A LEU 5.0 1.3 - - - -
31A PHE* 3.1 6.2 - - - +
32A MET* 2.8 56.6 + - + +
34A MET* 4.0 9.9 - - - -
49A ASP* 6.1 0.2 - - + -
51A PHE* 3.6 35.2 - + + -
59A VAL* 5.1 0.7 - - + -
61A ALA* 3.5 17.2 - - + +
64A GLY 3.3 12.7 + - - -
65A ILE 3.5 1.2 - - - -
66A THR* 2.9 43.3 + - - -
16B HIS* 3.1 41.7 - + + -
17B LEU* 4.1 3.6 - - + -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.6 24.9 - + + -
19A TYR* 1.3 80.3 - - - +
21A GLU* 1.3 60.4 + - - +
22A TYR* 4.1 20.1 + - + +
30A LEU 3.6 1.6 - - - -
31A PHE* 3.9 16.8 - + + -
64A GLY 4.5 0.3 - - - +
15B GLN 4.3 1.4 - - - +
16B HIS* 2.7 36.7 + - - +
18B TRP* 4.0 22.4 - + + +
20B PHE* 3.8 27.6 - + - -
20C PHE* 5.7 0.2 - + - -
20D PHE* 3.9 29.8 - + - -
31D PHE* 3.4 38.6 - + + -
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.7 16.4 - - + +
20A PHE* 1.3 73.3 - - - +
22A TYR* 1.3 72.2 + - - +
23A TYR* 4.2 12.7 - - + -
29A GLY* 3.0 4.7 - - - -
30A LEU* 2.8 59.1 + - - +
64A GLY 3.5 16.6 - - - +
65A ILE* 3.8 12.9 - - + +
66A THR* 2.9 40.2 + - - +
238A THR 4.5 3.6 - - - +
240A PRO* 4.4 15.2 - - - +
31D PHE* 3.5 1.7 - - - -
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Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.3 17.1 - - + +
21A GLU* 1.3 83.9 - - - +
23A TYR* 1.3 64.3 + - - +
26A ASN* 3.5 42.4 - - + +
28A VAL 4.0 2.2 - - - -
29A GLY* 4.3 0.2 - - - -
64A GLY 4.6 2.7 + - - +
65A ILE* 5.4 6.1 - - - +
15B GLN* 3.9 36.8 + - + -
18B TRP* 5.7 2.9 + - - -
22C TYR* 4.7 9.0 + - - -
15D GLN* 5.8 1.4 + - - -
18D TRP* 4.1 22.1 - + - -
31D PHE* 3.6 31.2 - + - -
33D LYS* 5.6 0.4 - - - -
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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