Contacts of the strand formed by residues 16 - 21 (chain L) in PDB entry 1I5L
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 PRO 16 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14L LYS 4.7 0.9 - - - +
15L SER* 1.3 91.0 + - - +
17L VAL* 1.3 67.5 + - - +
29L GLY* 3.3 12.3 - - - +
30L THR* 4.4 4.9 - - - +
72L PRO* 4.0 13.5 - - - +
73L ALA 5.5 0.9 - - - +
74L PRO 4.7 17.1 - - - +
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Residues in contact with VAL 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L SER* 4.6 10.8 - - - -
15L SER* 3.9 15.0 - - - +
16L PRO* 1.3 85.3 - - - +
18L ILE* 1.3 68.2 + - - +
19L VAL* 4.4 10.1 - - + -
27L PHE 3.9 0.3 - - - +
28L ARG* 3.4 5.5 - - - +
29L GLY 2.8 40.3 + - - +
31L LEU* 4.0 24.5 - - + -
42L LEU* 4.1 15.3 - - + -
70L VAL* 4.4 13.9 - - + -
71L SER 3.5 14.8 - - - +
72L PRO* 4.2 10.1 - - + -
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Residues in contact with ILE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 1.3 79.6 - - - +
19L VAL* 1.3 68.3 + - - +
20L ARG 3.8 0.6 + - - +
26L GLU* 4.4 24.5 - - + +
27L PHE 3.3 7.4 - - - +
28L ARG* 3.7 40.4 - - + +
69L PHE* 3.8 9.1 - - + +
70L VAL* 3.5 3.1 - - - -
71L SER* 2.8 39.7 + - - +
72L PRO 4.6 2.9 - - - +
73L ALA* 4.3 21.5 - - + +
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Residues in contact with VAL 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 4.4 3.8 - - + -
18L ILE* 1.3 76.0 - - - +
20L ARG* 1.3 60.6 + - - +
21L LEU* 3.7 23.7 + - + +
26L GLU* 3.3 3.4 - - - -
27L PHE* 2.7 44.3 + - + +
40L LEU* 3.8 33.2 - - + -
42L LEU* 3.9 26.9 - - + -
62L ILE* 4.2 4.7 - - + -
67L VAL* 3.9 9.4 - - + -
69L PHE 3.7 3.1 - - - +
70L VAL* 4.2 17.5 - - + -
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Residues in contact with ARG 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ILE* 3.8 2.2 + - - +
19L VAL* 1.3 71.6 - - - +
21L LEU* 1.3 73.1 + - - +
24L GLY* 4.0 17.3 + - - -
25L ARG 3.9 5.2 + - - -
26L GLU* 3.0 43.0 + - - +
67L VAL* 4.0 1.2 - - - +
68L VAL* 3.0 35.5 + - + +
69L PHE* 3.0 46.5 + - + +
25M ARG* 3.8 28.5 - - - +
47M GLU* 3.5 10.5 + - - -
55M ARG* 3.0 32.9 - - - +
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Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K VAL* 4.4 11.9 - - + -
69K PHE* 5.3 0.9 - - + -
19L VAL* 3.9 28.3 - - + +
20L ARG* 1.3 80.3 - - - +
22L LYS* 1.3 72.6 + - - +
24L GLY* 3.5 11.6 + - - -
25L ARG* 2.9 28.4 + - + +
27L PHE* 3.8 31.0 - - + -
62L ILE* 4.0 16.2 - - + -
66L THR* 3.5 33.4 - - + +
67L VAL* 4.0 2.7 - - + -
68L VAL* 3.5 9.9 - - - +
25M ARG* 5.1 2.4 + - - -
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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