Contacts of the strand formed by residues 51 - 57 (chain C) in PDB entry 1A81
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 PHE 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C SER* 4.8 7.9 - - - -
10C ALA* 3.6 33.7 - - + -
16C PHE* 4.3 15.9 - + - -
41C LEU* 3.8 28.0 - - + -
42C ARG 3.7 0.2 - - - -
43C GLN* 4.6 4.0 - - + -
44C SER* 3.4 14.2 - - - +
49C GLY* 2.9 22.4 - - - -
50C GLY* 1.3 94.1 - - - -
52C ALA* 1.3 59.8 + - - +
65C THR* 3.6 4.2 + - - -
66C ILE* 2.7 50.8 + - + +
74C TYR* 4.1 26.5 - + - -
85C PRO* 4.7 11.7 - - + -
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Residues in contact with ALA 52 (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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40C LEU 4.0 0.5 - - - +
41C LEU* 2.6 30.6 - - - +
42C ARG* 2.6 58.6 + - - +
44C SER* 4.1 6.9 - - - +
51C PHE* 1.3 77.5 - - - +
53C LEU* 1.3 59.4 + - - +
54C SER 4.1 0.2 - - - -
64C TYR 3.3 10.5 - - - +
65C THR* 4.6 4.3 - - - -
66C ILE* 4.4 2.0 - - - +
181D PTR 5.1 7.2 - - + +
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Residues in contact with LEU 53 (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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39C TYR* 3.9 32.1 - - + -
40C LEU 3.8 11.9 - - - +
41C LEU* 5.3 4.5 - - + -
52C ALA* 1.3 74.7 - - - +
54C SER* 1.3 70.7 + - - +
55C VAL* 4.2 4.0 - - + -
62C HIS 3.2 2.3 - - - +
63C HIS* 3.2 3.4 - - - -
64C TYR* 2.4 66.1 + - + +
66C ILE* 4.5 14.4 - - + -
76C ILE* 5.1 6.7 - - + -
88C LEU* 5.2 9.4 - - + -
89C CYS* 5.2 9.4 - - - -
92C HIS* 6.0 0.2 - - - +
99C LEU* 4.5 15.0 - - + -
103C LEU* 4.4 22.7 - - + -
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Residues in contact with SER 54 (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 ALA* 4.4 3.5 - - - +
29C LEU* 4.2 17.1 - - - +
39C TYR* 3.1 4.2 - - - +
40C LEU* 3.0 45.5 + - - -
42C ARG* 3.6 15.6 + - - +
52C ALA 4.1 0.2 - - - -
53C LEU* 1.3 73.3 - - - +
55C VAL* 1.3 61.4 + - - +
62C HIS 3.1 5.4 - - - -
63C HIS* 2.6 35.8 + - - -
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Residues in contact with VAL 55 (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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29C LEU* 4.5 4.9 - - - +
37C GLY 4.9 3.4 - - - +
38C LEU 2.9 4.5 - - - +
39C TYR* 2.9 31.0 - - + -
53C LEU* 4.2 6.1 - - + +
54C SER* 1.3 74.7 - - - +
56C ALA* 1.3 62.5 + - - +
62C HIS* 2.8 55.3 + - + +
64C TYR* 4.2 22.9 - - + -
99C LEU* 4.4 8.7 - - + -
100C VAL* 4.4 7.9 - - + -
101C CYS* 5.0 6.3 - - - -
103C LEU* 3.5 23.6 - - + -
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Residues in contact with ALA 56 (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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29C LEU* 4.4 7.3 - - + +
34C MET* 3.8 35.4 - - + +
35C SER 3.5 15.9 - - - +
36C ASP* 3.1 3.8 - - - -
37C GLY* 2.6 33.4 + - - -
38C LEU* 2.6 20.8 + - + +
55C VAL* 1.3 70.1 - - - +
57C HIS* 1.3 58.6 + - - +
58C GLY 4.2 0.2 - - - -
60C LYS 3.8 6.1 - - - -
61C ALA* 4.9 0.2 - - - +
101C CYS* 4.6 0.5 - - - -
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Residues in contact with HIS 57 (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 ASP* 3.2 24.9 - - + +
55C VAL 3.6 2.6 + - - +
56C ALA* 1.3 77.0 - - - +
58C GLY* 1.3 69.0 + - - +
59C ARG 4.6 0.6 - - - +
60C LYS* 3.2 13.1 + - - +
62C HIS* 3.0 34.1 + + + +
100C VAL* 4.1 24.8 + - + -
101C CYS* 3.5 34.8 - - + +
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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