Contacts of the strand formed by residues 601 - 606 (chain H) in PDB entry 3AOI
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 GLY 601 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599H GLU 3.7 1.0 + - - -
600H ASP* 1.3 78.4 - - - +
602H GLU* 1.3 61.3 + - - +
614H ARG 3.5 7.6 - - - -
615H TYR* 4.1 2.2 - - - -
616H GLU* 3.4 25.2 - - - +
648H ARG* 3.4 9.7 - - - +
649H VAL* 3.2 31.2 + - - +
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Residues in contact with GLU 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601H GLY* 1.3 74.8 - - - +
603H VAL* 1.3 81.9 + - - +
613H VAL* 2.9 8.0 - - - +
614H ARG* 2.6 79.9 + - - +
615H TYR* 5.6 0.2 - - - -
616H GLU* 4.7 8.9 + - - +
646H GLY* 4.1 16.7 - - - -
647H GLN 3.3 14.3 + - - +
648H ARG* 5.0 9.1 - - + +
649H VAL* 4.5 2.2 - - - +
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Residues in contact with VAL 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602H GLU* 1.3 93.6 - - - +
604H ALA* 1.3 68.1 + - - +
605H LYS 4.1 1.3 - - - +
606H VAL* 3.3 33.0 - - + -
611H ILE* 4.7 2.2 - - + -
612H VAL 4.0 2.5 - - - +
613H VAL* 3.1 22.2 - - + -
614H ARG* 4.8 2.2 + - - -
643H VAL* 3.6 26.9 - - + -
644H VAL 3.8 2.2 - - - +
646H GLY* 3.2 26.0 + - - +
647H GLN 3.2 15.5 + - - +
649H VAL* 4.0 7.6 - - + -
655H LEU* 5.9 0.9 - - + -
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Residues in contact with ALA 604 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLU* 5.5 0.2 - - - +
603H VAL* 1.3 75.7 - - - +
605H LYS* 1.3 68.1 + - + +
612H VAL* 2.8 28.3 + - + +
613H VAL* 3.8 6.6 - - - +
614H ARG* 4.8 12.6 - - + +
620H LEU* 6.3 0.7 - - + -
645H VAL* 3.0 23.9 - - - +
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Residues in contact with LYS 605 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLU* 3.3 27.6 - - + +
134F GLU* 6.2 5.4 - - + -
603H VAL* 4.1 0.2 - - - +
604H ALA* 1.3 85.3 - - + +
606H VAL* 1.3 63.3 + - - +
607H ASP 3.6 1.1 - - - -
610H ARG* 3.5 28.0 - - - +
611H ILE* 3.4 4.7 - - - +
612H VAL* 2.8 44.8 + - + +
622H GLU* 5.6 0.9 - - - +
645H VAL* 4.5 0.4 - - - -
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Residues in contact with VAL 606 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F LYS* 4.3 18.8 + - + +
133F GLU* 3.2 15.5 + - + +
603H VAL* 3.3 30.3 - - + -
605H LYS* 1.3 71.4 - - - +
607H ASP* 1.3 66.2 + - - +
610H ARG 4.1 1.8 - - - -
611H ILE* 4.4 11.7 - - + -
641H PRO* 5.4 5.4 - - + -
643H VAL* 3.4 26.2 - - + +
644H VAL* 3.7 7.0 - - - -
645H VAL* 3.4 35.7 - - + +
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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