Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 1I8F
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.2 5.6 - - + -
27B LYS 4.2 1.3 - - - +
28B LEU* 3.8 17.3 - - + -
45B VAL* 4.3 7.2 - - + +
47B LEU* 4.7 4.3 - - + -
68B VAL* 4.2 9.4 - - + -
69B ARG 3.5 16.6 - - - +
70B GLY* 2.9 21.2 + - - +
72B ASN* 1.3 78.2 - - - +
74B LEU* 1.4 62.5 + - - +
75B PHE* 3.6 22.9 - - - +
76B ILE* 3.9 20.2 - - + -
69C ARG* 3.0 38.8 + - + +
72C ASN* 3.1 6.3 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 2.8 17.0 + - + +
28B LEU 3.5 27.1 - - - +
29B ARG* 3.9 15.5 - - - +
73B VAL* 1.4 75.2 - - - +
75B PHE* 1.3 70.4 + - + +
28C LEU* 4.1 15.0 - - + +
29C ARG 4.2 11.9 - - - +
30C ASP* 4.9 0.2 - - - +
32C HIS* 3.3 40.8 - - + +
68C VAL* 3.6 7.8 - - - +
69C ARG* 3.2 23.9 + - - +
72C ASN* 3.7 34.0 - - + +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.1 24.5 - - + -
26B VAL* 3.5 5.5 - - - +
27B LYS* 3.3 44.8 + - + -
73B VAL* 3.6 3.1 - - - +
74B LEU* 1.3 90.2 - - + +
76B ILE* 1.3 74.6 + - - +
77B SER* 4.2 4.9 - - - -
28C LEU* 4.6 1.6 - - + -
32C HIS* 5.0 5.6 - - - -
34C ILE* 3.9 24.7 - - + -
54C GLU* 3.6 38.6 - - + -
63C ARG* 5.2 0.4 - - + -
66C MET* 3.6 30.3 - - + -
67C VAL 3.1 15.7 - - - +
68C VAL* 4.2 3.8 - - + -
69C ARG 4.9 0.7 - - - +
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Residues in contact with ILE 76 (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 LEU* 6.1 0.7 - - + -
15B THR* 6.1 1.1 - - + -
16B LEU* 4.4 19.7 - - + -
19B SER* 5.9 0.9 - - - +
24B VAL* 3.9 30.5 - - + -
25B LEU 3.4 4.5 - - - +
26B VAL* 4.3 6.3 - - + -
38B LEU* 5.6 4.7 - - + -
45B VAL* 3.8 27.8 - - + -
47B LEU* 3.9 28.5 - - + -
73B VAL* 3.9 11.9 - - + -
75B PHE* 1.3 79.2 - - - +
77B SER* 1.3 63.8 + - - +
78B PRO* 4.1 5.2 - - + +
66C MET* 3.5 0.9 - - - -
67C VAL* 2.9 43.0 + - + +
69C ARG* 6.3 0.4 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 4.2 1.8 - - - -
25B LEU* 2.8 45.2 + - - +
75B PHE* 4.2 17.9 - - - -
76B ILE* 1.3 77.1 - - - +
78B PRO* 1.4 66.8 + - - +
79B VAL* 3.2 0.9 + - - -
63C ARG* 3.3 31.9 + - - +
65C THR 2.8 18.9 + - - -
66C MET* 4.2 5.6 - - - -
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Residues in contact with PRO 78 (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 THR* 4.5 9.2 - - + -
19B SER* 3.9 24.2 - - - +
22B LYS* 5.2 11.0 - - + -
23B GLN 3.5 10.8 - - - +
24B VAL* 4.0 9.2 - - + -
76B ILE* 4.1 5.8 - - + +
77B SER* 1.4 84.5 + - - +
79B VAL* 1.3 67.0 + - - +
80B PRO* 3.3 9.0 - - - +
63C ARG 3.6 7.6 - - - +
65C THR* 3.4 32.3 + - + +
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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