Contacts of the strand formed by residues 377 - 381 (chain D) in PDB entry 4G3D
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 ASN 377 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D GLY* 3.0 22.5 + - - +
344D SER* 3.7 4.0 + - - -
345D VAL* 3.7 3.2 + - - +
376D ASP* 1.3 76.5 + - - +
378D GLU* 1.3 59.3 - - - +
391D TYR 4.5 2.1 - - - +
392D GLU* 3.5 14.8 - - + +
393D TYR 2.9 32.0 + - - -
394D ARG* 3.5 34.2 - - - +
459D VAL* 3.3 18.4 - - - +
460D ARG 2.8 24.1 + - - -
461D GLU* 3.6 14.1 - - + +
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Residues in contact with GLU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU 4.7 1.6 - - - +
342D GLN* 3.8 17.7 - - - +
343D GLY* 2.9 34.6 + - - +
344D SER 3.4 9.0 - - - +
345D VAL* 3.7 5.4 - - - -
356D LEU* 4.4 10.4 - - + +
359D THR* 4.8 3.5 - - - +
360D TRP* 3.0 27.5 + - + +
376D ASP* 5.3 0.3 - - - +
377D ASN* 1.3 73.9 - - - +
379D GLY* 1.3 58.9 + - - +
459D VAL* 3.6 0.7 - - - -
460D ARG* 2.8 72.0 + - - +
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Residues in contact with GLY 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU* 5.1 0.3 - - - +
344D SER 2.9 11.3 + - - +
345D VAL* 3.5 10.4 - - - +
346D SER* 3.0 23.8 + - - -
356D LEU* 3.9 13.3 - - - +
360D TRP* 4.1 2.5 - - - -
378D GLU* 1.3 75.8 - - - +
380D VAL* 1.3 68.2 + - - +
458D ALA 3.5 11.9 - - - -
459D VAL* 4.2 3.1 - - - -
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Residues in contact with VAL 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU* 5.0 4.5 - - + -
346D SER* 3.4 12.3 - - - +
347D SER 4.5 0.4 - - - -
348D GLY* 3.8 24.5 - - - +
349D GLN 4.1 6.7 - - - +
352D SER* 4.1 9.6 - - - -
353D LEU* 3.8 34.4 - - + +
356D LEU* 4.0 13.7 - - + -
379D GLY* 1.3 79.5 - - - +
381D LEU* 1.3 63.3 + - - +
382D LEU* 3.8 22.9 - - + -
457D GLY* 3.5 3.1 - - - -
458D ALA 3.0 31.1 + - - +
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Residues in contact with LEU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D VAL* 3.9 18.2 - - + -
346D SER 3.0 9.4 + - - +
347D SER* 3.4 10.1 - - - +
348D GLY 3.2 20.8 + - - -
380D VAL* 1.3 75.1 - - - +
382D LEU* 1.3 63.6 + - - +
383D THR 3.5 1.2 + - - +
386D LEU* 3.5 57.9 - - + +
387D LYS 4.1 0.2 - - - -
388D PRO* 3.9 21.1 - - + -
393D TYR* 4.0 16.8 - - + -
456D TYR 4.1 1.3 - - - -
457D GLY* 4.7 1.6 - - - -
459D VAL* 4.2 8.5 - - + -
468D PHE* 3.9 26.7 - - + -
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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
------------------------------------------------------------
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