Contacts of the strand formed by residues 23 - 27 (chain 4) in PDB entry 3EXG
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 VAL 23 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164 GLU* 4.4 7.6 - - + +
174 LEU* 3.1 26.1 - - + +
194 ARG* 6.2 0.2 - - - +
204 ASP* 3.1 21.5 + - + +
214 GLU 3.0 1.2 - - - -
224 LYS* 1.3 74.5 - - - +
244 PHE* 1.3 63.4 + - - +
514 ARG* 2.9 24.9 + - - -
754 ARG* 3.5 30.3 - - + +
774 ILE* 4.2 20.6 - - + -
1614 ILE* 3.8 27.6 - - + -
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Residues in contact with PHE 24 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503 LEU* 4.2 15.5 - - + -
1543 TYR* 4.0 19.3 - + + +
174 LEU* 4.1 5.6 - - - -
224 LYS 3.9 12.6 - - - -
234 VAL* 1.3 76.9 - - - +
254 LEU* 1.3 66.0 + - - +
264 LEU* 4.5 19.5 - - + -
504 LYS 4.9 1.1 - - - -
514 ARG* 3.4 21.8 - - - +
534 ILE* 3.8 30.1 - - + -
664 ALA* 5.4 1.3 - - - -
694 ALA* 3.9 18.8 - - + -
744 LEU* 3.8 27.1 - - + -
754 ARG 3.7 2.0 + - - -
764 PRO* 3.9 21.3 - - + -
774 ILE* 2.8 29.8 + - - +
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Residues in contact with LEU 25 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134 MET* 4.3 15.5 - - + -
174 LEU* 5.2 3.1 - - + -
244 PHE* 1.3 79.2 - - - +
264 LEU* 1.3 69.4 + - - +
304 VAL* 4.2 22.4 - - + -
404 SER* 4.2 24.2 - - - -
434 LEU* 4.4 7.2 - - + -
514 ARG 2.8 14.5 + - - +
524 ILE* 3.6 20.8 - - + -
534 ILE* 3.1 22.5 + - - +
774 ILE* 3.4 40.2 - - + +
794 GLU* 4.3 8.3 - - + -
1154 ARG* 4.4 5.8 - - - +
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Residues in contact with LEU 26 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1503 LEU* 5.5 0.9 - - + -
1853 TRP* 4.7 9.2 - - + -
244 PHE* 4.5 16.4 - - + -
254 LEU* 1.3 75.5 - - - +
274 GLY* 1.3 59.4 + - - +
304 VAL* 3.9 6.1 - - - -
534 ILE* 3.3 26.0 - - + +
554 THR* 4.1 14.6 - - + -
624 PHE* 4.4 21.9 - - + +
654 ILE* 4.4 18.4 - - + -
664 ALA* 3.7 19.7 - - + -
764 PRO* 4.8 1.3 - - + -
774 ILE 3.0 18.9 + - - +
784 CYS* 3.7 15.3 - - + -
794 GLU* 3.0 27.0 + - - +
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Residues in contact with GLY 27 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264 LEU* 1.3 76.6 - - - +
284 GLU* 1.3 60.3 + - - -
304 VAL* 3.5 11.4 - - - +
534 ILE 3.1 9.2 + - - +
544 ASP* 3.3 2.6 - - - -
554 THR* 2.7 39.4 + - - +
624 PHE* 4.3 5.4 - - - -
794 GLU 3.8 13.7 - - - -
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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