Contacts of the strand formed by residues 613 - 621 (chain A) in PDB entry 5TFM
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 LEU 613 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A SER* 3.8 6.2 + - - -
609A ILE* 3.5 13.3 - - - +
610A SER* 3.7 8.7 + - - +
611A ASN* 3.2 32.2 - - + +
612A GLY* 1.3 83.1 - - - +
614A ILE* 1.3 65.0 + - - +
615A TYR* 3.2 40.8 - - + +
635A THR* 3.8 22.2 - - + -
636A ILE 3.4 1.1 - - - -
637A GLU* 4.1 21.5 - - + +
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Residues in contact with ILE 614 (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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581A SER* 3.2 11.9 - - - +
582A ALA* 3.7 28.0 - - + +
583A PHE* 4.7 2.0 - - + -
587A PHE* 3.8 24.5 - - + -
604A LEU* 4.1 16.4 - - + -
609A ILE* 3.9 32.8 - - + -
613A LEU* 1.3 79.6 - - - +
615A TYR* 1.3 65.6 + - - +
616A LEU* 3.9 22.2 - - + -
635A THR* 3.6 2.4 - - - +
636A ILE* 2.8 47.5 + - + +
638A VAL* 4.4 4.9 - - + -
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Residues in contact with TYR 615 (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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579A SER* 4.1 3.3 + - - -
580A ALA* 3.3 3.1 + - - -
581A SER* 2.8 48.7 + - - -
611A ASN* 4.9 3.6 + - - +
613A LEU* 3.2 36.6 - - + +
614A ILE* 1.3 75.1 - - - +
616A LEU* 1.3 63.3 + - - +
634A VAL 3.5 4.7 - - - +
635A THR* 4.0 30.1 - - + -
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Residues in contact with LEU 616 (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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577A ILE* 4.5 16.8 - - + -
579A SER 3.5 6.7 - - - +
580A ALA* 3.5 31.4 - - + -
587A PHE* 4.1 32.1 - - + -
598A ILE* 4.3 23.1 - - + -
614A ILE* 3.9 13.4 + - + -
615A TYR* 1.3 78.3 - - - +
617A THR* 1.3 66.1 + - - +
618A VAL* 5.0 1.1 - - + -
633A PRO* 3.6 4.2 - - - +
634A VAL* 2.9 38.9 + - + +
636A ILE* 4.3 18.8 - - + -
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Residues in contact with THR 617 (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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577A ILE* 3.6 3.6 - - - +
578A VAL* 2.9 36.1 + - + -
579A SER* 3.0 32.8 + - - -
616A LEU* 1.3 75.4 + - - +
618A VAL* 1.3 64.3 + - - +
631A THR* 3.7 31.6 - - + +
632A VAL 3.5 9.4 - - - +
633A PRO* 5.1 1.9 - - + +
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Residues in contact with VAL 618 (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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538A PHE* 3.9 11.0 - - + -
560A LEU* 3.9 19.1 - - + -
575A TYR* 4.4 4.5 - - + -
576A SER 3.3 12.6 - - - +
577A ILE* 4.7 7.0 - - + -
589A ILE* 3.9 21.5 - - + -
598A ILE* 3.9 18.6 - - + -
616A LEU* 5.0 2.2 - - + -
617A THR* 1.3 77.3 - - - +
619A MET* 1.3 67.8 + - - +
631A THR* 3.1 6.0 - - - -
632A VAL* 2.9 36.5 + - + +
634A VAL* 3.6 25.6 - - + -
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Residues in contact with MET 619 (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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538A PHE* 4.1 2.5 - - - -
574A THR* 3.4 2.2 - - + +
575A TYR* 3.3 5.7 - - - -
576A SER* 2.8 52.0 + - - +
578A VAL* 3.5 25.4 - - + -
618A VAL* 1.3 74.5 - - - +
620A ALA* 1.3 58.2 + - - +
621A MET* 3.8 41.5 - - + +
629A ASN* 3.7 31.2 - - + +
630A SER 3.3 13.9 - - - +
631A THR* 4.4 8.3 - - + -
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Residues in contact with ALA 620 (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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536A PRO* 3.9 9.8 - - + +
538A PHE* 3.6 23.7 - - + -
562A ALA* 3.7 23.8 - - + -
573A ILE* 3.7 12.1 - - + -
574A THR 3.4 5.2 - - - -
575A TYR* 4.0 5.6 - - + -
619A MET* 1.3 71.4 - - - +
621A MET* 1.3 62.2 + - - +
628A LEU 4.0 0.2 - - - +
629A ASN* 3.1 25.6 - - - +
630A SER 3.0 12.0 + - - +
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Residues in contact with MET 621 (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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536A PRO* 4.3 2.2 - - - -
572A GLN 3.7 0.7 - - - +
573A ILE* 3.5 3.1 - - - +
574A THR* 2.9 47.4 + - + +
619A MET* 3.8 30.5 - - + +
620A ALA* 1.3 77.5 - - - +
622A ASP* 1.3 66.0 + - - +
627A PRO* 3.7 33.2 - - + -
628A LEU 3.3 17.3 - - - +
629A ASN* 4.2 4.7 - - + -
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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