Contacts of the strand formed by residues 31 - 39 (chain C) in PDB entry 2Z9I
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 GLU 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU 3.8 1.0 - - - +
23C GLU* 3.5 3.5 - - - +
24C THR* 2.9 37.9 + - - +
30C SER* 1.3 75.1 - - - +
32C GLU* 1.3 70.9 + - - +
49C HIS* 3.9 26.6 - - - +
50C VAL* 4.3 21.5 - - - +
53C ALA* 5.8 8.5 - - + -
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Residues in contact with GLU 32 (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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21C MSE 3.7 10.0 - - + +
22C LEU 3.5 3.8 - - - +
23C GLU* 3.8 27.1 - - + +
30C SER* 4.0 3.1 + - - +
31C GLU* 1.3 84.4 + - - +
33C GLY* 1.3 65.6 + - - +
50C VAL* 4.6 3.4 - - - +
122C SER* 2.7 42.8 - - - +
124C LEU* 4.3 2.6 + - - -
125C GLY* 3.5 17.5 + - - -
166C PRO 4.7 0.5 - - - -
167C GLY* 3.4 22.4 + - - +
411F VAL 4.2 5.2 - - - +
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Residues in contact with GLY 33 (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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21C MSE 3.6 4.9 - - - +
22C LEU 3.0 27.7 + - - +
32C GLU* 1.3 86.1 - - - +
34C SER* 1.3 64.2 + - - -
50C VAL* 3.8 15.6 - - - +
167C GLY 3.5 13.9 - - - -
169C SER 3.6 7.0 - - - -
411F VAL 4.8 0.9 - - - -
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Residues in contact with SER 34 (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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19C VAL* 4.6 1.3 - - - -
20C VAL 3.2 12.6 - - - -
22C LEU* 3.6 9.7 - - - +
33C GLY* 1.3 74.4 - - - -
35C GLY* 1.3 53.9 + - - +
46C THR* 2.7 28.1 + - - -
50C VAL* 4.4 0.3 - - - +
121C GLY* 3.5 7.0 - - - -
122C SER* 3.0 18.7 + - - -
167C GLY 2.7 23.6 + - - -
168C ASN 3.7 1.4 + - - -
169C SER 2.7 10.9 + - - +
170C GLY 3.4 3.6 - - - +
171C GLY* 3.5 26.9 - - - -
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Residues in contact with GLY 35 (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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19C VAL* 3.4 8.5 - - - +
20C VAL* 2.9 39.9 + - - +
22C LEU* 4.1 2.0 - - - -
34C SER* 1.3 76.3 - - - +
36C ILE* 1.3 64.9 + - - -
44C ILE* 3.8 13.9 - - - -
45C LEU 3.2 11.4 - - - -
170C GLY 3.3 2.5 - - - -
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Residues in contact with ILE 36 (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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18C SER 3.5 4.7 - - - +
19C VAL* 4.6 0.9 - - + +
35C GLY* 1.3 80.1 - - - +
37C ILE* 1.3 65.8 + - - +
38C LEU* 3.2 2.5 + - + +
44C ILE* 3.4 4.4 - - - +
45C LEU* 2.8 44.0 + - + +
103C ILE* 3.6 45.5 - - + -
170C GLY 3.5 16.2 - - - +
171C GLY 3.6 24.5 - - - +
172C ALA* 3.8 6.5 - - + +
180C LEU* 3.8 20.9 - - + -
183C VAL* 3.8 23.6 - - + -
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Residues in contact with ILE 37 (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 PRO 3.5 25.6 - - - +
18C SER* 2.6 14.6 + - - +
20C VAL* 3.8 26.0 - - + -
35C GLY 4.2 0.2 - - - -
36C ILE* 1.3 68.7 - - - +
38C LEU* 1.3 56.4 + - - +
39C SER 3.5 24.2 - - - +
42C GLY* 5.2 0.4 - - - -
43C LEU 3.7 6.5 - - - +
44C ILE* 4.3 9.9 - - + -
70C PHE* 3.8 19.1 - - + -
100C LEU* 4.4 21.3 - - + -
101C THR 3.6 21.5 - - - +
102C PRO* 3.3 6.2 - - + +
103C ILE* 2.8 37.1 + - - +
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Residues in contact with LEU 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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36C ILE* 3.2 4.8 + - + +
37C ILE* 1.3 73.3 - - - +
39C SER* 1.3 59.1 + - - +
43C LEU* 2.8 19.1 + - + +
44C ILE 4.6 0.7 - - - -
45C LEU* 3.7 49.1 - - + +
91C VAL* 4.6 8.1 - - + -
102C PRO* 3.4 13.5 - - - +
103C ILE* 4.7 9.9 - - + +
105C LEU* 4.4 24.9 - - + -
217C ALA* 4.4 12.6 - - + -
221C ILE* 4.2 24.5 - - + -
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Residues in contact with SER 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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37C ILE* 3.5 10.5 - - - +
38C LEU* 1.3 79.6 - - - +
40C ALA* 1.3 59.4 + - - +
41C GLU* 3.7 20.6 + - - +
42C GLY* 2.9 26.3 + - - -
43C LEU* 3.3 36.0 + - - +
102C PRO* 4.0 7.6 - - - -
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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