Contacts of the strand formed by residues 670 - 676 (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 ILE 670 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A ALA* 3.6 18.7 + - + +
669A ILE* 1.3 79.7 - - - +
671A TYR* 1.3 66.6 + - - +
720A LEU* 3.8 24.2 - - + -
749A LYS* 3.8 28.0 - - + -
750A ILE 3.2 9.9 - - - +
751A LYS* 4.2 14.8 - - + +
676B LYS* 3.3 29.2 + - + +
706B LEU* 5.8 3.0 - - - +
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Residues in contact with TYR 671 (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 ILE* 4.8 0.2 - - + -
670A ILE* 1.3 77.2 - - - +
672A THR* 1.3 61.9 + - - +
673A VAL* 3.2 34.3 - - + -
712A ALA 2.7 19.3 + - - -
713A ILE* 3.9 1.7 - - - +
714A HIS* 5.0 0.3 + - - -
717A ASP* 3.7 15.4 + - - -
749A LYS* 3.6 1.0 - - - +
750A ILE* 2.7 64.0 + - + +
752A LYS* 3.8 21.3 - - + -
673B VAL* 4.1 11.0 - - + -
674B GLU 3.5 9.4 - - - +
675B LEU* 4.0 14.1 - - + -
676B LYS* 3.6 7.2 - - - +
706B LEU* 6.4 0.2 - - + -
710B THR* 3.8 28.0 + - + -
712B ALA* 3.5 16.7 - - + +
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Residues in contact with THR 672 (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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671A TYR* 1.3 79.9 + - - +
673A VAL* 1.3 68.1 + - - +
747A THR* 3.3 31.9 - - + -
748A LEU 3.3 8.3 - - - +
749A LYS* 3.8 22.7 - - + +
673B VAL* 3.5 3.6 - - - +
674B GLU* 2.8 51.2 + - + +
676B LYS* 3.5 15.9 + - - +
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Residues in contact with VAL 673 (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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671A TYR* 3.2 33.0 - - + -
672A THR* 1.3 78.2 - - - +
674A GLU* 1.3 61.1 + - - +
675A LEU* 4.6 10.1 - - + -
712A ALA* 4.0 17.9 - - + +
713A ILE* 3.9 22.7 - - + -
746A VAL 3.7 0.9 - - - +
747A THR* 3.3 3.6 - - - +
748A LEU* 2.8 53.9 + - + +
750A ILE* 4.4 2.2 - - + -
671B TYR* 5.2 0.7 - - + -
672B THR 3.2 6.7 - - - +
673B VAL* 4.1 16.6 - - + -
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Residues in contact with GLU 674 (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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672A THR* 6.2 0.2 - - + -
673A VAL* 1.3 72.6 - - - +
675A LEU* 1.3 64.8 + - - +
676A LYS 4.1 0.5 + - - -
745A THR* 4.3 29.1 + - + +
746A VAL 3.5 4.7 - - - +
747A THR* 3.7 20.0 + - + +
671B TYR* 3.6 7.3 - - - +
672B THR* 2.8 51.2 + - + +
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Residues in contact with LEU 675 (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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673A VAL* 4.6 10.5 - - + -
674A GLU* 1.3 74.8 - - - +
676A LYS* 1.3 61.6 + - - +
677A ARG* 3.6 2.0 + - - +
682A LEU* 4.2 22.9 - - + -
706A LEU* 4.3 18.8 - - + -
707A ALA* 5.5 2.9 - - - -
710A THR* 4.0 26.0 - - + +
712A ALA* 4.1 9.9 - - + -
713A ILE* 4.3 16.8 - - + -
745A THR* 3.2 5.4 - - - -
746A VAL* 2.8 42.8 + - - +
748A LEU* 4.2 23.1 - - + -
671B TYR* 4.1 20.0 - - + -
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Residues in contact with LYS 676 (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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674A GLU 4.1 2.0 + - - -
675A LEU* 1.3 72.2 - - - +
677A ARG* 1.3 57.8 + - - +
678A TYR* 3.0 58.6 - - + +
706A LEU* 3.4 12.1 - - - +
744A GLU* 3.3 40.1 + - + +
745A THR* 4.3 11.8 - - + +
670B ILE* 4.2 17.4 + - + +
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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