Contacts of the strand formed by residues 45 - 51 (chain C) in PDB entry 4YHP
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 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C VAL* 4.6 9.6 - - + -
38C ARG 3.7 3.1 - - - +
39C GLN* 3.8 33.4 - - + +
44C GLY* 1.3 73.0 - - - -
46C GLU* 1.3 60.0 + - - +
95C TYR* 4.9 3.1 - - + -
111C TRP* 4.7 2.2 - - + -
35D TYR* 5.1 2.2 - - + -
37D GLN* 4.3 0.2 - - - +
43D PRO* 3.8 35.7 - - + -
86D TYR* 3.7 34.1 - - + -
99D PHE* 3.6 58.5 - - + +
100D GLY 5.2 1.1 + - - +
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Residues in contact with GLU 46 (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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37C VAL* 3.7 3.6 - - - +
38C ARG* 2.6 91.8 + - + +
44C GLY 5.0 1.6 - - - +
45C LEU* 1.3 76.4 - - - +
47C TRP* 1.3 69.7 + - - +
61C ILE* 4.0 15.7 - - + +
63C ALA* 4.9 4.0 - - - +
99D PHE* 4.5 0.2 - - - -
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Residues in contact with TRP 47 (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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35C SER* 3.1 22.8 + - - -
36C TRP 3.8 9.9 - - - -
37C VAL* 3.9 8.5 - - + +
46C GLU* 1.3 76.1 - - - +
48C VAL* 1.3 61.3 + - - +
49C ALA* 3.4 9.5 + - - -
50C ASP* 3.2 33.4 - - - -
59C TYR* 3.4 32.1 - - + -
60C TYR 3.9 1.6 - - - -
61C ILE* 3.3 63.2 - - + +
108C PHE* 3.6 13.7 - + - -
90D TRP* 4.7 2.2 - + - -
95D ASN 4.2 2.9 - - - -
96D ALA* 3.7 18.8 - - + -
97D TYR* 3.3 56.7 + + + +
99D PHE* 4.1 13.1 - - + -
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Residues in contact with VAL 48 (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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36C TRP* 2.9 25.2 + - + +
37C VAL 4.3 0.4 - - - -
38C ARG* 3.6 44.4 - - + +
46C GLU 3.7 2.2 - - - +
47C TRP* 1.3 79.6 - - - +
49C ALA* 1.3 67.1 + - + +
60C TYR* 3.5 2.1 - - - -
61C ILE* 3.2 30.6 + - + +
64C VAL* 3.9 12.6 - - + +
68C PHE* 3.7 32.8 - - + -
81C LEU* 4.3 8.1 - - + -
94C TYR* 4.4 6.1 - - + -
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Residues in contact with ALA 49 (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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35C SER* 3.3 2.8 - - - -
36C TRP* 2.9 27.7 + - + -
47C TRP* 3.4 9.1 + - - -
48C VAL* 1.3 90.0 - - + +
50C ASP* 1.3 61.5 + - - +
59C TYR 3.1 13.2 - - - +
60C TYR* 3.6 24.9 - - + -
70C ILE* 3.9 16.3 - - + +
81C LEU* 4.5 6.7 - - + -
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Residues in contact with ASP 50 (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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33C TRP* 3.3 18.3 - - - -
34C MET 3.2 6.5 - - - +
35C SER* 3.1 13.7 - - - +
47C TRP* 3.2 18.4 - - + -
49C ALA* 1.3 71.6 - - - +
51C ILE* 1.3 62.4 + - - +
58C ARG* 3.3 6.9 - - - +
59C TYR* 3.0 38.9 + - - +
70C ILE* 3.6 7.2 - - - +
99C GLU* 2.7 30.6 - - - +
97D TYR* 4.1 1.4 - - - -
9Q M3L 3.5 14.2 - - - -
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Residues in contact with ILE 51 (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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33C TRP* 3.4 7.2 - - - -
34C MET 3.0 24.1 + - - +
50C ASP* 1.3 75.8 - - - +
52C ASN* 1.3 72.8 + - - +
55C GLY* 3.6 29.4 - - - +
57C THR 3.4 4.7 - - - +
58C ARG* 3.8 14.1 - - + +
70C ILE* 3.7 15.5 - - + +
71C SER* 3.7 28.0 - - - -
72C ARG* 3.3 17.3 + - + +
79C LEU* 3.5 31.0 - - + -
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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