Contacts of the strand formed by residues 105 - 109 (chain 1) in PDB entry 3EPD
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 105 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921 VAL* 4.1 2.2 - - - -
1031 LYS* 3.8 12.7 - - - -
1041 LEU* 1.3 79.1 - - + +
1061 ALA* 1.3 54.7 + - - +
1071 MET* 4.2 5.8 - - + -
1671 PRO* 3.4 37.5 - - + -
1681 LYS 3.7 6.3 - - - -
1691 SER* 3.6 19.5 - - - -
1701 TRP* 3.5 18.4 - - + -
1751 TRP* 3.8 17.9 - + + -
2431 VAL 3.1 14.4 - - - +
2441 ARG* 4.0 3.4 - - + -
130R GLN* 1.8 66.7 - - + +
133R ARG* 3.1 32.1 - - + -
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Residues in contact with ALA 106 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 ILE* 3.5 28.5 - - + -
911 GLU 3.6 18.6 - - - +
921 VAL* 4.7 2.9 - - + -
1031 LYS* 5.8 0.2 - - + -
1051 PHE* 1.3 64.8 - - - +
1071 MET* 1.3 56.5 + - - +
2411 LEU 3.8 0.3 - - - +
2421 ALA* 3.3 3.6 - - - +
2431 VAL* 2.9 32.6 + - + +
130R GLN* 1.7 38.6 - - + +
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Residues in contact with MET 107 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 ILE* 5.5 1.5 - - - +
1051 PHE* 4.2 2.7 - - + -
1061 ALA* 1.3 76.1 - - - +
1081 TRP* 1.3 52.9 + - - +
1601 ILE* 3.6 21.5 - - + -
1661 THR* 3.9 0.4 - - + -
1671 PRO* 3.7 7.6 - - + -
2401 VAL* 3.5 17.3 - - + -
2411 LEU 3.2 4.9 - - - +
2421 ALA* 3.8 6.5 - - + -
127R THR 3.8 0.7 - - - -
128R PHE 2.5 5.5 - - - +
129R PRO* 1.9 39.7 - - - +
130R GLN* 2.4 36.3 - - - +
131R GLY 3.5 7.4 - - - +
132R SER* 2.1 91.1 - - - +
133R ARG* 4.2 1.1 - - - -
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Residues in contact with TRP 108 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871 VAL* 3.9 20.0 - - + -
881 ALA* 3.5 25.0 - - + +
901 ILE* 3.6 26.0 - - + +
1071 MET* 1.3 70.4 - - - +
1091 ARG* 1.3 61.1 + - - +
1101 ILE* 3.4 20.8 + - + -
1111 THR 3.2 39.0 - - - -
1141 ASP* 3.0 3.8 + - - -
1341 PHE* 4.7 2.7 - + - -
2401 VAL* 3.1 4.6 - - - -
2411 LEU* 2.9 46.9 + - + +
2601 ILE* 3.7 27.6 - - + -
2621 MET* 4.2 5.8 - - + -
128R PHE* 2.2 61.4 - + - +
129R PRO* 5.5 0.2 - - + -
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Residues in contact with ARG 109 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081 TRP* 1.3 72.6 - - - +
1101 ILE* 1.3 69.3 + - - +
1111 THR* 3.3 2.2 + - - +
2351 VAL 4.8 1.3 - - - -
2361 ASP* 2.9 39.8 + - - +
2371 ASP* 5.2 9.0 - - + -
2391 GLY* 3.6 11.5 + - - +
2401 VAL* 3.6 19.1 - - + +
61R VAL* 2.3 44.1 - - + +
63R GLN* 3.3 13.2 + - - +
126R VAL* 2.8 51.3 - - - +
127R THR 3.8 2.3 + - - +
128R PHE* 3.1 45.4 + - + +
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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