Contacts of the strand formed by residues 59 - 64 (chain C) in PDB entry 4JRI
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 ILE 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.6 27.8 - - + -
25C TYR 3.7 8.3 - - - +
26C LEU* 4.2 1.1 - - + +
27C VAL* 4.3 2.2 - - - -
44C ILE* 3.6 33.0 - - + -
54C VAL* 3.8 18.6 - - + -
55C TYR 3.7 8.7 - - - +
56C LYS* 3.0 21.6 + - - +
58C ALA* 1.3 79.0 - - - +
60C SER* 1.3 62.6 + - - +
61C THR 3.7 10.8 - - - +
62C VAL* 3.9 7.9 - - + -
55D TYR* 3.6 25.9 - - + +
57D HIS* 3.0 25.8 + - - -
58D ALA* 3.9 0.3 - - - +
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Residues in contact with SER 60 (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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25C TYR* 2.7 31.6 + - - +
26C LEU 3.7 11.1 + - - -
27C VAL* 4.6 4.5 - - - -
58C ALA 3.9 2.0 + - - -
59C ILE* 1.3 74.6 - - - +
61C THR* 1.3 69.6 + - - +
26D LEU* 3.8 26.3 - - - +
27D VAL* 6.3 0.2 - - - -
28D ASN* 4.7 3.5 + - - -
30D ILE* 5.9 0.2 - - - +
54D VAL* 3.4 3.8 - - - +
55D TYR 2.8 27.5 + - - +
58D ALA* 3.5 21.1 - - - -
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Residues in contact with THR 61 (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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24C ILE* 3.7 1.7 - - - -
25C TYR* 2.9 48.0 + - - +
59C ILE* 3.7 1.6 - - - +
60C SER* 1.3 91.0 + - - +
62C VAL* 1.3 65.7 + - - +
63C VAL* 4.1 1.0 - - - +
26D LEU* 4.2 6.5 - - + +
32D LEU* 3.5 34.0 - - + +
52D GLN* 3.4 20.6 + - - +
53D MET 3.2 7.0 - - - -
54D VAL* 3.8 9.6 - - + -
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Residues in contact with VAL 62 (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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11C PHE* 4.1 4.5 - - + -
12C LEU* 4.6 7.2 - - + -
15C LEU* 4.3 23.8 - - + -
22C VAL* 4.6 8.3 - - + -
23C SER 3.5 7.9 - - - +
24C ILE* 4.4 17.9 - - + -
36C ILE* 5.3 0.7 - - + -
44C ILE* 4.8 10.1 - - + -
59C ILE* 3.9 17.5 - - + -
61C THR* 1.3 77.4 - - - +
63C VAL* 1.3 62.8 + - - +
64C PRO* 3.7 3.5 - - - +
52D GLN* 3.5 3.8 - - - -
53D MET* 2.8 57.2 + - + +
55D TYR* 4.3 4.5 - - + -
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Residues in contact with VAL 63 (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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22C VAL* 4.6 2.5 - - - -
23C SER* 2.8 40.9 + - - +
25C TYR* 4.0 25.6 - - + +
61C THR* 4.1 4.7 - - - +
62C VAL* 1.3 77.4 - - - +
64C PRO* 1.3 76.3 - - - +
65C SER* 3.5 0.9 + - - -
50D VAL* 3.9 26.9 - - + -
52D GLN* 3.7 29.6 - - + +
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Residues in contact with PRO 64 (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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11C PHE* 3.8 15.0 - - + -
15C LEU* 3.6 32.5 - - + -
20C VAL* 4.5 0.4 - - + -
21C PRO 4.2 4.9 - - - +
22C VAL* 4.5 2.7 - - + -
62C VAL 3.7 6.5 - - - +
63C VAL* 1.3 96.7 - - - +
65C SER* 1.3 65.6 + - - +
66C ARG 3.3 19.3 - - - +
67C PRO* 5.0 0.7 - - + -
68C VAL* 4.0 10.8 - - + -
50D VAL* 3.5 16.7 - - + +
51D SER 3.6 21.3 - - - +
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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