Contacts of the helix formed by residues 705 - 711 (chain A) in PDB entry 1N7F
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 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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683A GLY* 4.7 6.3 - - - -
702A THR* 2.9 26.5 + - - -
703A LYS 3.2 2.6 + - - -
704A GLY* 1.3 80.5 - - - +
706A LEU* 1.3 60.8 + - - -
707A ALA 3.4 2.2 - - - -
708A GLU* 3.3 3.1 + - - +
709A ARG* 2.9 31.6 + - - +
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Residues in contact with LEU 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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675A LEU* 4.3 20.4 - - + -
676A LYS 3.4 28.9 - - - +
677A ARG* 3.6 22.9 - - + +
678A TYR* 4.6 8.7 - - + -
681A PRO 3.9 12.4 + - - +
682A LEU* 3.4 20.0 + - + +
683A GLY* 4.6 0.2 - - - -
705A GLY* 1.3 70.4 - - - -
707A ALA* 1.3 65.5 + - - +
709A ARG* 3.3 20.6 + - - +
710A THR* 3.0 48.6 + - + +
669B ILE* 4.4 12.6 - - + -
670B ILE 6.0 0.2 - - - +
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Residues in contact with ALA 707 (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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675A LEU* 5.5 3.8 - - + -
682A LEU* 2.8 14.1 + - + +
683A GLY 3.9 4.3 - - - +
684A ILE* 3.2 34.8 - - + -
701A LEU* 4.1 8.5 - - + -
705A GLY 3.4 0.4 - - - -
706A LEU* 1.3 74.1 - - - +
708A GLU* 1.3 57.9 + - - +
710A THR* 3.0 7.1 + - - -
711A GLY* 3.0 27.0 + - - -
712A ALA 3.8 2.6 + - - -
713A ILE* 3.8 24.8 - - + +
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Residues in contact with GLU 708 (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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683A GLY 5.2 0.2 + - - -
701A LEU* 4.3 26.7 - - + +
702A THR 3.8 11.9 + - - +
703A LYS* 3.4 33.2 + - - +
704A GLY* 2.7 30.4 + - - +
705A GLY 3.3 8.3 + - - +
706A LEU 3.3 0.4 - - - -
707A ALA* 1.3 80.0 - - - +
709A ARG* 1.3 62.4 + - + +
711A GLY* 3.3 12.7 + - - -
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Residues in contact with ARG 709 (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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678A TYR* 6.2 1.4 - - - -
704A GLY* 3.3 28.2 + - - +
705A GLY* 2.9 15.1 + - - +
706A LEU* 3.9 24.8 - - - +
708A GLU* 1.3 78.2 - - + +
710A THR* 1.3 61.6 + - - +
669B ILE* 3.8 34.3 - - + +
752B LYS* 3.3 20.1 - - - +
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Residues in contact with THR 710 (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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675A LEU* 4.0 11.4 - - + +
706A LEU* 3.0 26.7 + - + +
707A ALA* 3.0 13.0 + - - -
709A ARG* 1.3 77.8 - - + +
711A GLY* 1.3 65.4 + - - +
712A ALA* 3.1 22.9 + - - +
669B ILE* 3.5 27.6 - - + -
671B TYR* 3.7 22.6 + - + -
714B HIS* 3.9 0.7 - - - -
752B LYS* 2.8 30.0 + - - +
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Residues in contact with GLY 711 (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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707A ALA 3.0 10.1 + - - -
708A GLU* 3.3 10.9 + - - -
710A THR* 1.3 79.9 + - - +
712A ALA* 1.3 58.8 + - - +
713A ILE 3.5 2.9 - - - -
714A HIS* 3.1 25.3 - - - -
711B GLY 3.1 2.9 - - - +
712B ALA* 3.5 1.0 - - - -
714B HIS* 2.8 29.6 - - - -
752B LYS* 5.0 0.7 - - - -
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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