Contacts of the strand formed by residues 672 - 676 (chain B) in PDB entry 4P3N
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 672 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B PHE* 3.5 34.8 - + - -
620B GLN 3.0 8.7 + - - +
621B VAL* 3.3 10.5 - - + +
622B MET* 2.9 24.3 + - - +
670B TYR* 4.3 1.6 - - - +
671B ASN* 1.3 93.1 - - + +
673B ILE* 1.3 65.1 + - - +
674B LEU* 4.0 14.5 + - + -
688B ILE* 4.3 17.9 - - + -
689B ARG 3.6 4.3 - - - +
690B THR* 5.1 5.2 - - + -
696B HIS* 5.9 0.2 - - - -
704B THR* 6.4 0.4 - - + -
708B LEU* 3.5 25.4 - - + -
711B LEU* 4.1 4.3 - - + -
719B ALA* 4.0 25.4 - - + -
720B GLU* 4.2 13.9 - - + -
723B PHE* 3.8 23.6 - + + -
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Residues in contact with ILE 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B MET* 3.4 12.8 - - + +
624B VAL* 4.6 8.5 - - + -
662B ILE* 4.3 18.8 - - + +
665B ALA* 3.6 29.8 - - + -
666B GLN* 4.2 13.5 - - + +
670B TYR* 3.8 18.8 - - + +
672B PHE* 1.3 77.7 - - - +
674B LEU* 1.3 62.4 + - - +
675B VAL* 3.7 22.4 + - + -
687B ASN 3.5 1.9 - - - +
688B ILE* 3.9 0.5 - - - -
689B ARG* 2.9 48.3 + - + +
690B THR 3.8 20.6 - - - +
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B VAL* 3.7 27.1 - - + -
622B MET 2.9 11.0 + - - +
623B VAL* 3.4 13.3 - - + +
624B VAL 2.9 26.2 + - - +
637B VAL* 4.5 5.8 - - + -
641B PHE* 3.5 40.6 - - + -
672B PHE* 4.6 10.1 - - + -
673B ILE* 1.3 76.8 - - - +
675B VAL* 1.3 62.8 + - - +
676B VAL* 4.9 0.4 - - + -
686B VAL* 4.2 19.1 - - + -
687B ASN 3.6 2.5 - - - -
688B ILE* 4.1 29.8 - - + -
704B THR* 4.5 6.5 - - + -
708B LEU* 5.8 1.3 - - + -
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Residues in contact with VAL 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B VAL* 3.3 8.3 - - + +
626B VAL* 3.9 18.2 - - + -
658B LEU* 3.8 26.9 - - + -
662B ILE* 3.9 21.3 - - + -
673B ILE* 3.9 21.8 - - + +
674B LEU* 1.3 74.8 - - - +
676B VAL* 1.3 64.7 + - - +
680B GLU* 3.9 2.9 - - - +
687B ASN* 2.9 56.3 + - + +
689B ARG* 5.1 3.8 - - + -
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Residues in contact with VAL 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 4.3 5.2 - - + -
624B VAL 2.9 18.7 + - - +
625B PRO* 3.4 5.2 - - + +
626B VAL* 2.8 35.1 + - - +
630B CYS* 4.1 5.2 - - + +
633B TYR* 3.5 34.3 - - + -
634B ALA* 3.7 31.6 - - + +
637B VAL* 4.4 5.4 - - + -
674B LEU 4.7 3.6 - - - +
675B VAL* 1.3 79.9 - - - +
677B GLY* 1.3 55.6 + - - +
680B GLU* 3.6 3.4 - - - -
685B THR 3.9 2.5 - - - +
686B VAL* 3.8 23.6 - - + -
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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