Contacts of the helix formed by residues 628 - 633 (chain A) in PDB entry 3NR8
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 PHE 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A ILE* 3.8 32.5 - - + -
626A LYS* 3.7 26.7 + - + -
627A GLU* 1.3 76.5 - - - +
629A GLU* 1.3 60.4 + - - +
630A PRO 3.4 0.2 - - - -
631A LEU* 3.1 8.7 + - + +
632A LEU* 2.9 42.3 + - + +
655A ILE 4.8 2.7 - - - +
656A SER* 4.1 19.5 - - - -
657A PHE 3.7 11.0 - - - -
658A PRO* 3.4 45.8 - - + -
688A TRP* 4.1 17.5 - + + -
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Residues in contact with GLU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A PHE* 1.3 76.5 - - - +
630A PRO* 1.3 73.9 - - + +
632A LEU* 3.1 19.1 + - + +
633A ARG* 2.5 63.4 + - + +
633B ARG* 5.2 1.2 + - - -
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Residues in contact with PRO 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A MET* 3.6 16.7 - - + +
622A TYR* 3.8 45.1 - - + +
627A GLU* 3.8 17.5 - - + +
628A PHE 3.7 1.6 - - - -
629A GLU* 1.3 98.5 - - + +
631A LEU* 1.3 59.7 + - - +
633A ARG* 3.8 16.9 + - + +
634A VAL* 4.3 1.9 + - - +
642B GLU* 4.5 3.6 - - + +
644B HIS* 5.5 2.5 - - + -
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Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU* 3.5 15.6 - - + +
614A MET* 3.6 20.4 - - - -
619A ILE* 3.9 26.7 - - + +
622A TYR* 3.6 37.2 - - + -
623A ILE* 3.6 31.6 - - + +
627A GLU 4.1 7.9 - - - +
628A PHE* 3.1 9.1 + - + +
630A PRO* 1.3 73.0 - - - +
632A LEU* 1.3 65.8 + - - +
633A ARG 3.2 1.8 - - - -
634A VAL* 3.1 14.3 + - - +
635A ASP 3.2 9.4 + - - -
659A PRO* 5.0 0.2 - - + -
688A TRP* 3.8 22.4 - - + -
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Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A PHE* 2.9 30.0 + - + +
629A GLU* 3.5 18.6 - - - +
631A LEU* 1.3 77.0 - - - +
633A ARG* 1.3 59.3 + - - +
634A VAL 3.1 2.0 + - - -
635A ASP* 3.6 6.3 + - + -
638A ASN* 3.2 41.4 + - - +
642A GLU* 5.6 0.2 - - - +
655A ILE* 3.2 59.2 - - + +
688A TRP* 4.1 18.6 - - + -
691A ARG* 5.6 0.4 - - - +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A GLU* 2.5 41.3 + - - +
630A PRO* 4.0 11.7 - - + +
631A LEU 3.2 1.0 - - - -
632A LEU* 1.3 76.3 - - - +
634A VAL* 1.3 61.3 + - - +
635A ASP 3.7 0.2 - - - -
638A ASN* 5.8 1.1 - - - +
639A LEU* 3.5 21.2 - - - +
642A GLU* 5.2 6.7 - - - +
629B GLU* 4.6 1.8 + - - -
633B ARG* 3.2 42.9 - - - +
639B LEU* 5.1 0.7 - - - +
642B GLU* 3.2 48.0 + - + +
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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