Contacts of the strand formed by residues 36 - 45 (chain C) in PDB entry 3G33
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 36 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C VAL* 5.1 13.5 - - + -
27C LYS* 3.9 33.7 - - + -
28C ALA 3.2 17.3 - - - +
29C ARG* 3.4 29.6 - - + -
34C GLY 5.1 5.4 - - - -
35C HIS* 1.3 78.4 - - - +
37C VAL* 1.3 62.0 + - - +
99C GLU* 5.0 0.2 - - - -
100C HIS* 3.1 43.1 + + + +
102C ASP* 5.8 0.2 - - - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.7 32.5 - - + -
26C TYR 3.6 0.3 - - - +
27C LYS* 3.7 2.3 - - - -
28C ALA* 2.8 53.6 + - + +
29C ARG 4.5 1.3 - - - +
30C ASP* 4.5 6.5 - - + +
35C HIS* 4.4 9.2 - - + +
36C PHE* 1.3 80.2 - - - +
38C ALA* 1.3 60.3 + - - +
39C LEU* 3.6 5.3 + - + -
80C MET* 5.0 10.5 - - + -
97C VAL* 3.7 21.5 - - + -
98C PHE 3.5 11.7 - - - +
99C GLU* 5.5 0.7 - - - -
100C HIS* 3.5 5.2 - - - +
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Residues in contact with ALA 38 (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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17C ILE* 4.0 22.0 - - + -
25C VAL* 4.2 7.9 - - + -
26C TYR 3.5 4.9 - - - -
37C VAL* 1.3 69.6 - - - +
39C LEU* 1.3 64.5 + - - +
40C LYS* 3.4 2.2 + - - +
96C LEU 3.4 2.9 - - - +
98C PHE* 2.9 48.2 + - + +
99C GLU 4.8 1.3 - - - +
100C HIS* 3.5 15.5 - - + +
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Residues in contact with LEU 39 (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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10C ARG* 5.7 5.2 - - - -
11C TYR* 4.4 18.4 - - + +
13C PRO* 4.8 11.2 - - + -
24C THR 4.2 1.2 - - - +
25C VAL* 3.5 7.3 - - - +
26C TYR* 2.7 55.2 + - + +
28C ALA* 3.8 27.4 - - + -
37C VAL* 3.6 6.0 + - + -
38C ALA* 1.3 69.9 - - - +
40C LYS* 1.3 59.0 + - - +
41C SER* 4.2 1.8 - - - +
95C THR* 3.9 16.2 - - + -
96C LEU 4.0 0.7 - - - -
97C VAL* 3.8 35.7 - - + -
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Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 4.4 10.7 - - + +
24C THR 4.9 2.9 - - - +
25C VAL* 3.9 32.9 - - + +
38C ALA* 4.4 2.4 - - - +
39C LEU* 1.3 73.3 - - - +
41C SER* 1.3 61.3 + - - +
95C THR* 4.2 1.2 - - - +
96C LEU* 2.7 53.0 + - + +
98C PHE* 4.2 28.3 - - + +
162C ALA* 6.0 0.6 - - - +
163C ASP* 2.4 43.3 + - - +
166C LEU* 4.5 6.0 - - + +
170C TYR* 3.0 30.3 - - + +
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Residues in contact with SER 41 (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 TYR 4.4 6.9 - - - +
24C THR 4.7 9.1 + - - +
26C TYR* 5.5 9.2 - - - -
39C LEU* 4.2 2.0 + - - +
40C LYS* 1.3 73.0 + - - +
42C VAL* 1.3 72.6 + - - +
93C LYS* 5.8 6.7 - - - -
94C VAL 3.4 6.7 - - - -
95C THR* 3.3 22.6 + - - +
170C TYR* 3.9 4.3 + - - -
173C GLN* 4.1 6.3 + - - +
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Residues in contact with VAL 42 (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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41C SER* 1.3 76.6 - - - +
43C ARG* 1.3 59.0 + - - +
44C VAL* 3.8 7.1 + - + -
93C LYS* 3.5 4.1 - - - -
94C VAL* 2.7 58.5 + - + +
96C LEU* 4.1 10.3 - - + -
169C ILE* 4.0 25.1 - - + +
170C TYR* 2.3 54.3 - - + +
173C GLN* 3.5 14.1 - - + +
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Residues in contact with ARG 43 (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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42C VAL* 1.3 73.1 - - - +
44C VAL* 1.3 60.6 + - - +
91C GLU* 3.7 32.1 + - - +
92C ILE 3.4 5.2 - - - +
93C LYS* 4.1 25.2 - - + +
169C ILE 5.7 1.0 - - - +
172C TYR* 3.6 24.3 + - + +
173C GLN* 3.4 26.7 + - + +
176C LEU* 3.8 34.5 - - - +
177C THR* 4.4 10.1 + - - -
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Residues in contact with VAL 44 (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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150B TRP* 6.0 1.8 - - + -
42C VAL* 4.3 10.1 - - + +
43C ARG* 1.3 76.9 - - - +
45C PRO* 1.3 106.5 - - + +
54C LEU* 5.1 1.8 - - + -
55C PRO* 3.4 17.7 - - + -
58C THR* 4.2 20.2 - - + +
91C GLU* 2.8 28.3 - - - +
92C ILE* 2.5 34.1 + - + +
94C VAL* 3.6 27.1 - - + -
169C ILE* 5.3 2.7 - - + +
172C TYR* 5.6 3.1 - - - -
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Residues in contact with PRO 45 (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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44C VAL* 1.3 106.4 - - + +
46C ASN* 1.3 59.5 + - - +
47C GLY 5.2 6.3 - - - +
53C GLY 3.6 5.3 - - - +
54C LEU* 3.3 22.2 - - - +
55C PRO* 3.1 28.5 - - + +
58C THR* 5.0 0.9 - - - +
90C ARG 4.9 1.8 - - - +
91C GLU* 4.7 2.0 - - + -
92C ILE* 4.8 1.0 - - - +
172C TYR* 5.5 16.2 - - + -
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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