Contacts of the strand formed by residues 670 - 676 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676A LYS* 4.2 21.3 + - + +
678A TYR* 3.0 18.7 + - - +
706A LEU* 6.0 0.7 - - - +
710A THR* 5.5 0.2 - - - +
668B ALA* 5.0 7.4 - - + -
669B ILE* 1.3 84.6 - - - +
671B TYR* 1.3 68.3 + - - +
672B THR* 5.4 0.2 - - - +
720B LEU* 3.7 24.7 - - + -
749B LYS* 3.8 37.2 - - + -
750B ILE 3.2 11.7 - - - +
751B LYS* 4.2 12.1 - - + -
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Residues in contact with TYR 671 (chain B).
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* 5.1 1.1 - - + -
674A GLU 3.6 12.8 - - - +
675A LEU* 4.1 15.0 - - + -
676A LYS 5.3 0.2 - - - +
710A THR* 3.7 29.3 + - + -
712A ALA* 3.6 26.0 - - + -
670B ILE* 1.3 80.5 - - - +
672B THR* 1.3 63.5 + - - +
673B VAL* 3.3 29.4 - - + -
712B ALA 2.7 21.5 + - - -
713B ILE* 4.5 0.9 - - - -
714B HIS* 3.9 6.4 + - - -
717B ASP* 4.2 4.3 + - - -
749B LYS* 3.7 0.3 - - - -
750B ILE* 2.7 63.0 + - + +
752B LYS* 3.6 26.7 - - + -
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Residues in contact with THR 672 (chain B).
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* 3.2 6.2 - - - +
674A GLU* 2.8 58.7 + - + +
670B ILE* 5.4 0.5 - - - +
671B TYR* 1.3 76.9 + - - +
673B VAL* 1.3 68.7 + - - +
674B GLU* 5.0 0.4 - - + +
747B THR* 3.2 34.3 - - + -
748B LEU 3.2 10.5 - - - +
749B LYS* 3.9 18.7 - - + +
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Residues in contact with VAL 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A TYR* 4.1 13.2 - - + -
672A THR 3.5 6.5 - - - +
673A VAL* 4.1 8.1 - - + -
671B TYR* 3.3 34.8 - - + -
672B THR* 1.3 79.2 - - - +
674B GLU* 1.3 60.6 + - - +
675B LEU* 3.8 27.8 + - + +
712B ALA* 4.0 12.6 - - + +
713B ILE* 4.0 19.1 - - + -
746B VAL 3.6 2.4 - - - +
747B THR* 3.4 1.0 - - - -
748B LEU* 2.8 40.9 + - + +
750B ILE* 4.3 4.3 - - + -
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Residues in contact with GLU 674 (chain B).
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* 3.5 5.4 - - - +
672A THR* 2.8 39.8 + - + +
672B THR* 5.9 0.2 - - + -
673B VAL* 1.3 72.5 - - - +
675B LEU* 1.3 60.1 + - - +
676B LYS* 2.6 40.0 + - - +
745B THR* 3.2 32.4 - - + +
746B VAL 3.4 3.4 - - - -
747B THR* 3.9 18.7 + - + +
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Residues in contact with LEU 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ILE 5.6 0.2 - - - -
671A TYR* 4.0 6.1 - - + -
673B VAL* 3.8 24.2 - - + +
674B GLU* 1.3 76.1 - - - +
676B LYS* 1.3 66.5 + - - +
677B ARG 3.6 2.1 + - - -
682B LEU* 3.9 29.4 - - + -
684B ILE* 4.4 20.0 - - + -
706B LEU* 4.2 12.3 - - + -
707B ALA* 4.7 7.6 - - - -
710B THR* 3.9 29.6 - - + +
713B ILE* 4.5 13.2 - - + -
745B THR* 3.3 3.8 - - - +
746B VAL* 2.7 43.9 + - + +
748B LEU* 4.7 7.6 - - + -
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Residues in contact with LYS 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A ILE* 3.3 35.2 + - + +
671A TYR* 3.6 4.3 - - - +
672A THR* 3.5 15.9 + - - +
749A LYS* 6.5 0.2 - - - +
674B GLU* 2.6 57.0 + - - +
675B LEU* 1.3 73.1 - - - +
677B ARG* 1.3 60.1 - - - +
678B TYR* 2.9 38.3 - - + +
706B LEU* 3.6 15.3 - - - +
744B GLU 3.5 7.9 - - - +
745B THR* 4.5 9.4 - - + +
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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