Contacts of the strand formed by residues 673 - 679 (chain A) in PDB entry 5IFE
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 VAL 673 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A PRO* 6.0 4.0 - - + -
667A ILE 3.8 0.5 - - - +
668A GLY* 3.5 2.8 - - - -
669A LEU* 3.0 61.2 + - + -
671A ASN* 2.6 29.3 + - - +
672A GLY* 1.3 80.8 - - - +
674A LEU* 1.3 59.5 + - - +
675A LEU* 3.8 11.4 - - + -
688A ASP* 5.7 4.5 - - + +
689A THR 3.3 11.2 - - - +
690A ARG* 4.8 10.1 - - + -
691A THR 4.4 0.4 - - - +
699A VAL* 3.6 5.9 - - - +
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Residues in contact with LEU 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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666A ASN* 4.9 10.8 - - + +
667A ILE 3.2 14.1 - - - +
673A VAL* 1.3 74.4 - - - +
675A LEU* 1.3 68.0 + - - +
676A ARG* 5.1 8.1 - - + -
688A ASP* 3.0 7.3 - - - +
689A THR* 2.9 47.6 + - + +
691A THR* 4.1 15.0 + - - +
699A VAL* 4.0 10.3 - - + -
701A LEU* 3.6 35.2 - - + -
714A ALA* 4.2 9.6 - - + -
722A SER* 5.6 4.9 - - - -
731A LEU* 4.4 21.8 - - + -
1221A ASP* 5.8 1.8 - - - +
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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
----------------------------------------------------------
633A LEU* 4.7 16.4 - - + -
634A PRO* 4.8 13.2 - - + -
665A LEU 3.5 1.4 - - - +
666A ASN* 3.2 8.4 - - - +
667A ILE* 2.9 46.4 + - + +
669A LEU* 3.6 31.6 - - + -
673A VAL* 3.8 13.9 - - + -
674A LEU* 1.3 84.7 - - - +
676A ARG* 1.3 63.0 + - - +
677A THR* 4.6 4.0 - - - +
686A LEU* 3.6 28.3 - - + -
687A SER 3.0 7.4 - - - +
688A ASP* 3.8 13.9 - - + -
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Residues in contact with ARG 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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664A TYR* 4.5 19.2 - - + -
665A LEU 3.6 3.6 - - - -
666A ASN* 3.1 25.6 - - - +
674A LEU* 5.1 9.8 - - + +
675A LEU* 1.3 73.1 - - - +
677A THR* 1.3 65.0 + - - +
685A ASP 3.9 0.2 - - - +
686A LEU* 3.3 2.3 - - - -
687A SER* 2.9 50.4 + - - +
712A VAL* 6.1 0.9 - - - -
722A SER* 4.5 12.5 + - - -
729A PHE* 3.3 46.5 - - - +
1221A ASP* 2.3 43.6 + - - +
1222A ASP* 5.2 5.5 - - - +
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Residues in contact with THR 677 (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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631A GLN* 3.9 20.3 + - - +
664A TYR* 3.4 8.8 - - - -
665A LEU* 2.8 46.0 + - - +
667A ILE* 4.4 9.4 - - - +
675A LEU 4.6 0.3 - - - -
676A ARG* 1.3 78.8 + - - +
678A VAL* 1.3 64.1 + - - +
683A THR* 3.0 27.6 - - - +
684A GLY 4.1 9.6 - - - +
685A ASP 3.0 19.7 - - - +
686A LEU* 4.0 15.0 - - + +
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Residues in contact with VAL 678 (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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662A PHE* 5.9 3.1 - - - +
663A LEU 3.7 11.0 - - - +
664A TYR* 4.6 13.1 - - + -
677A THR* 1.3 72.6 - - - +
679A LEU* 1.3 67.4 + - - +
682A VAL 5.3 1.3 - - - +
683A THR* 2.3 37.7 + - - -
684A GLY* 3.4 9.0 - - - +
685A ASP* 3.1 41.6 + - + +
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Residues in contact with LEU 679 (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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604A PHE* 4.3 14.1 - - + -
616A ILE* 4.0 27.1 - - + -
642A ILE* 4.0 39.5 - - + -
662A PHE 5.4 1.2 + - - -
663A LEU* 3.1 44.7 + - + +
664A TYR 4.6 0.2 - - - +
665A LEU* 4.4 10.8 - - + +
677A THR 4.5 2.9 - - - +
678A VAL* 1.3 82.7 - - - +
680A ASP* 1.4 80.2 + - - +
682A VAL 4.0 5.4 - - - -
683A THR* 3.6 24.5 - - - +
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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