Contacts of the strand formed by residues 480 - 485 (chain A) in PDB entry 1IEQ
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 ALA 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LEU* 5.8 0.2 - - - +
414A LEU* 3.1 23.1 - - + +
479A TYR* 1.3 81.7 - - - +
481A ILE* 1.3 61.7 + - - +
482A VAL* 4.0 1.1 - - + -
512A VAL* 3.5 31.4 - - + -
516A VAL* 3.8 9.6 - - + -
517A ARG 2.9 8.1 + - - +
518A CYS* 3.3 2.0 - - + -
519A ALA* 2.8 33.4 + - - +
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Residues in contact with ILE 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 3.8 28.9 - - + -
413A ILE* 5.4 0.4 - - + -
414A LEU 2.8 9.6 + - - +
415A VAL* 3.2 11.0 - - + +
416A ALA 2.8 24.9 + - - +
420A ALA* 5.3 0.2 - - - +
447A ILE* 4.5 15.9 - - + -
451A VAL* 4.1 24.7 - - + -
479A TYR* 4.5 9.0 - - + -
480A ALA* 1.3 76.3 - - - +
482A VAL* 1.3 62.9 + - - +
483A ALA* 5.8 0.4 - - + -
519A ALA* 3.4 11.9 - - + +
521A VAL* 4.1 10.8 - - + -
557A LEU* 3.9 29.4 - - + -
558A PHE* 4.1 13.9 - - + -
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Residues in contact with VAL 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 3.0 17.9 - - + +
417A GLY* 4.1 3.4 - - - -
480A ALA* 4.7 0.2 - - + -
481A ILE* 1.3 78.4 - - - +
483A ALA* 1.3 62.5 + - - +
484A VAL* 4.2 4.0 - - + -
508A THR* 4.1 18.8 - - + -
509A VAL* 3.9 28.0 - - + -
512A VAL* 3.4 37.9 - - + -
518A CYS* 4.6 11.4 - - + -
519A ALA 3.1 6.4 + - - +
520A THR* 3.4 8.9 - - - +
521A VAL* 2.8 27.9 + - - +
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Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A ALA 2.8 9.3 + - - -
417A GLY* 3.1 13.5 - - - -
419A HIS* 3.0 33.7 + - + +
420A ALA* 3.5 26.9 - - + +
447A ILE* 3.8 21.5 - - + -
481A ILE* 4.2 0.9 - - + -
482A VAL* 1.3 73.0 - - - +
484A VAL* 1.3 61.4 + - - +
521A VAL* 3.3 11.4 - - + +
523A ILE* 5.1 0.2 - - + -
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Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLY* 4.3 6.7 - - - -
418A SER* 4.2 6.7 - - - +
419A HIS* 3.6 13.2 - - - +
482A VAL* 4.2 14.4 - - + -
483A ALA* 1.3 80.6 - - - +
485A GLY* 1.3 60.5 + - - +
501A ILE* 4.2 15.9 - - + -
504A PRO 4.6 1.1 - - - +
505A GLY* 3.7 33.2 - - - +
508A THR* 4.7 3.6 - - - -
509A VAL* 4.0 16.8 - - + -
520A THR* 4.5 5.8 - - + -
521A VAL 3.2 9.4 + - - +
522A LEU* 3.5 6.4 - - + +
523A ILE* 2.9 23.2 + - - +
533A LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A SER* 4.6 0.6 + - - -
419A HIS* 3.1 19.1 - - - -
484A VAL* 1.3 79.6 - - - +
486A GLU* 1.3 64.9 + - - -
487A HIS* 4.1 2.6 + - - -
501A ILE* 4.0 22.8 - - - +
502A PRO* 3.4 16.9 + - - +
522A LEU* 4.2 2.9 - - - -
523A ILE 3.0 11.2 - - - -
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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
------------------------------------------------------------
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