Contacts of the strand formed by residues 29 - 35 (chain G) in PDB entry 1I3R
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 ASP 29 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G ASP* 3.3 5.0 - - - -
26G PHE* 2.6 41.9 + - - +
27G ASP* 4.6 0.7 - - - +
28G GLY* 1.3 79.5 - - - +
30G GLU* 1.3 62.1 + - - +
138G LEU* 6.2 0.4 - - - -
149H TYR* 3.6 25.5 + - - -
175H ARG* 3.0 36.6 + - - +
177H GLY* 4.4 8.0 - - - +
179H TRP* 3.5 44.5 + - + +
180H THR 5.5 0.2 + - - -
181H PHE* 4.5 2.3 - - - -
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Residues in contact with GLU 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G MET* 3.7 17.7 - - + -
24G PHE 3.6 5.8 - - - -
25G ASP* 4.2 0.4 + - - -
29G ASP* 1.3 72.9 - - - +
31G ILE* 1.3 61.9 + - - +
32G PHE* 3.6 17.3 - - - +
33G HIS* 2.6 43.0 + - - +
44G ARG* 2.9 44.8 + - + +
135G THR* 4.5 7.1 - - - -
136G VAL* 3.7 13.7 + - - +
138G LEU* 4.0 18.3 - - + +
177H GLY 5.7 2.8 + - - +
179H TRP* 2.9 23.8 + - - +
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Residues in contact with ILE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ILE* 5.4 0.7 - - + -
24G PHE* 3.0 22.6 + - + +
25G ASP 4.3 4.7 - - - +
26G PHE* 3.8 26.7 - - + +
30G GLU* 1.3 74.2 - - - +
32G PHE* 1.3 78.1 + - + +
43G TRP* 3.7 17.9 - - + -
44G ARG* 2.9 21.8 + - - +
48G PHE* 3.8 18.6 - - + -
112H PHE* 3.6 32.3 - - + -
115H PHE* 5.2 1.6 - - + -
116H LEU* 3.6 30.5 - - + -
179H TRP* 4.3 1.8 - - + -
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Residues in contact with PHE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G PHE* 4.1 10.3 - + - -
23G MET* 3.2 4.9 - - - +
24G PHE* 3.0 66.4 + + + +
30G GLU* 3.6 9.0 - - - +
31G ILE* 1.3 87.9 - - + +
33G HIS* 1.3 68.2 + - - +
34G VAL* 4.2 4.0 - - + -
41G THR* 3.6 18.4 - - + -
42G ILE 3.2 18.6 - - - +
43G TRP* 3.9 27.1 - + + -
44G ARG 4.3 0.7 - - - +
54G PHE* 3.4 44.2 - + + -
5H ILE* 4.1 19.1 - - + -
112H PHE* 5.3 0.2 - + - -
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Residues in contact with HIS 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G GLU* 6.1 2.0 - - + -
22G PHE 3.0 15.3 - - - +
23G MET* 3.6 8.3 - - + -
30G GLU* 2.6 27.3 + - - +
32G PHE* 1.3 77.1 - - - +
34G VAL* 1.3 79.7 + - - +
35G ASP* 3.9 11.8 + - - -
42G ILE* 3.0 62.3 + - + +
44G ARG* 6.5 0.7 - - - -
135G THR* 6.0 0.7 - - - -
136G VAL* 3.5 35.3 - - + +
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLY 4.8 0.2 - - - +
21G GLU* 4.4 4.9 - - - +
22G PHE* 2.8 27.0 + - + +
32G PHE* 4.2 8.5 - - + -
33G HIS* 1.3 84.6 - - - +
35G ASP* 1.3 72.4 + - - +
36G ILE* 3.2 11.6 + - + +
40G GLU 3.9 4.5 - - - +
41G THR* 4.5 4.3 - - - -
54G PHE* 3.9 19.3 - - + -
56G ALA* 4.0 26.2 - - + +
59G ALA* 3.3 36.6 - - + -
60G LEU* 4.2 10.1 - - + -
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Residues in contact with ASP 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G HIS* 3.9 19.3 + - - -
34G VAL* 1.3 73.2 - - - +
36G ILE* 1.3 56.9 + - - +
37G GLU* 2.8 15.5 - - - +
38G LYS* 3.5 30.9 + - + +
39G SER* 2.7 34.4 + - - +
40G GLU* 3.5 12.5 + - + +
42G ILE* 4.3 9.2 - - + +
60G LEU* 4.1 0.2 - - - +
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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