Contacts of the helix formed by residues 701 - 706 (chain A) in PDB entry 3F2B
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 PRO 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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700A HIS* 1.4 87.9 - - + +
702A PRO* 1.4 67.5 - - + +
703A ASP* 4.5 3.1 - - + +
704A VAL* 2.9 35.9 + - + +
705A TYR* 3.8 2.6 - - - -
741A THR 3.4 14.4 - - - +
742A GLY* 4.3 3.6 - - - -
779A ARG* 3.8 32.8 - - - +
784A MET* 3.6 32.5 - - + -
787A CYS* 4.3 10.1 - - + -
788A PHE* 3.6 8.3 - - + -
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Residues in contact with PRO 702 (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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700A HIS 3.3 4.6 - - - +
701A PRO* 1.4 81.0 - - + +
703A ASP* 1.3 70.5 + - - +
704A VAL 3.2 0.7 + - - -
705A TYR* 3.2 17.4 + - + +
706A LYS* 3.9 4.2 + - - -
717A GLU* 4.7 20.2 - - + +
720A ILE* 4.4 13.7 - - + +
721A LYS* 4.8 13.7 - - + -
724A ILE* 4.2 17.9 - - + -
787A CYS* 3.7 27.6 - - + +
788A PHE* 4.4 6.3 - - + -
790A PHE* 4.6 9.9 - - + -
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Residues in contact with ASP 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A PRO* 3.2 2.1 + - + +
702A PRO* 1.3 78.8 - - - +
704A VAL* 1.3 54.3 + - + +
706A LYS* 2.7 41.7 + - + +
717A GLU* 5.2 5.4 - - - +
774A PRO* 4.8 2.2 - - - +
775A ASP* 4.7 17.4 - - + +
779A ARG* 4.0 23.9 + - - +
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A ASP* 5.7 2.0 - - - +
700A HIS* 3.9 28.7 - - + +
701A PRO* 2.9 32.5 + - + +
703A ASP* 1.3 69.8 - - - +
705A TYR* 1.3 59.7 + - + +
706A LYS 3.3 0.4 + - - -
707A PRO* 3.8 2.8 - - - +
742A GLY 4.3 4.9 - - - +
743A ASN* 5.0 6.1 - - + +
774A PRO* 3.3 28.5 - - + +
775A ASP 3.4 23.8 - - - +
776A VAL* 3.8 18.6 - - + -
779A ARG* 3.7 14.1 - - - +
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Residues in contact with TYR 705 (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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669A GLY 4.6 3.5 + - - -
670A CYS 4.8 0.2 - - - -
671A ASP* 4.0 26.0 - - + -
676A PHE* 3.3 47.4 - + + -
698A GLU 4.5 0.9 + - - -
699A VAL* 3.6 9.2 - - - +
700A HIS* 2.8 62.6 + - + +
701A PRO 3.8 8.1 - - - -
702A PRO* 3.2 4.6 + - + +
703A ASP 2.9 1.4 + - - -
704A VAL* 1.3 75.7 - - + +
706A LYS* 1.3 58.4 + - - +
707A PRO* 2.9 27.1 - - - +
708A LEU* 4.3 1.6 - - - +
720A ILE* 3.5 40.7 - - + +
724A ILE* 4.0 9.2 - - + -
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Residues in contact with LYS 706 (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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702A PRO 3.9 2.5 + - - +
703A ASP* 2.7 26.4 + - - +
705A TYR* 1.3 68.7 - - - +
707A PRO* 1.4 63.0 - - + +
708A LEU* 2.8 14.4 + - - +
720A ILE* 4.8 7.0 - - - -
774A PRO* 5.8 2.9 - - + -
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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