Contacts of the strand formed by residues 551 - 556 (chain A) in PDB entry 4FOV
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 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A GLU* 3.2 5.8 - - - +
547A LEU* 2.8 48.2 + - + -
548A ARG* 2.8 51.9 + - + +
549A ASP 4.1 5.6 - - - +
550A GLY* 1.3 78.7 - - - +
552A ILE* 1.3 60.0 + - - +
567A THR* 3.9 18.8 - - + -
568A SER 3.2 8.3 - - - +
569A ARG* 4.1 15.9 - - + +
634A ASP* 4.1 14.8 - - - +
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Residues in contact with ILE 552 (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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496A LEU* 3.8 15.7 - - + -
498A LEU* 4.3 9.4 - - + -
505A ILE* 3.7 22.2 - - + -
544A MET* 3.8 29.4 - - + -
545A VAL 3.3 6.5 - - - +
546A GLU* 4.8 2.5 - - + -
550A GLY 4.4 5.2 - - - +
551A VAL* 1.3 76.3 - - - +
553A ARG* 1.3 62.6 + - - +
566A MET 3.7 0.7 - - - +
567A THR* 3.3 7.4 - - - -
568A SER 2.7 37.7 + - - +
571A SER* 3.7 9.0 - - - -
572A GLY* 3.6 30.3 - - - +
575A TRP* 3.7 22.4 - - + -
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Residues in contact with ARG 553 (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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543A GLN 3.9 0.5 - - - +
544A MET* 3.4 1.2 - - - -
545A VAL* 2.7 52.9 + - + +
547A LEU* 3.8 23.0 - - + +
551A VAL 4.0 1.2 + - - -
552A ILE* 1.3 74.4 - - - +
554A THR* 1.3 68.5 + - - +
555A PHE* 3.8 27.5 + - + -
565A TYR* 3.5 33.6 - - + -
566A MET 3.5 7.2 - - - +
567A THR* 2.9 28.8 + - + +
569A ARG* 5.0 4.0 - - - +
633A ASP 5.0 1.0 + - - -
634A ASP* 2.8 37.7 + - - +
635A SER* 4.4 4.9 - - - +
636A ILE* 3.7 20.9 - - - +
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Residues in contact with THR 554 (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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514A LEU* 4.0 5.8 - - + -
516A TYR* 2.6 33.1 + - + +
542A ALA* 3.4 30.7 - - + -
543A GLN 3.4 8.7 - - - +
544A MET* 3.6 12.4 - - + +
553A ARG* 1.3 73.4 - - - +
555A PHE* 1.3 65.2 + - - +
556A PHE* 4.1 2.2 - - + -
565A TYR* 3.0 27.4 - - - +
566A MET* 2.9 15.5 + - - -
575A TRP* 3.2 15.9 - - - -
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Residues in contact with PHE 555 (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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542A ALA* 3.3 0.7 - - - -
543A GLN* 2.8 38.2 + - - +
545A VAL* 3.9 23.1 - - + -
553A ARG* 3.8 29.8 - - + -
554A THR* 1.3 72.6 - - - +
556A PHE* 1.3 60.0 + - - +
563A ILE* 4.2 8.1 - - + -
564A ALA 3.4 3.6 - - - +
565A TYR* 3.8 16.4 - + + -
581A ILE* 3.8 17.7 - - + -
593A VAL* 3.7 16.0 - - + +
595A ALA* 3.8 13.7 - - + -
608A VAL* 4.0 5.4 - - + -
610A LEU* 3.6 24.5 - - + -
636A ILE* 3.9 10.3 - - + -
638A TRP* 3.8 33.7 - + - -
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Residues in contact with PHE 556 (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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514A LEU* 3.9 13.2 - - + -
533A ILE* 3.6 33.2 - - + -
535A PHE* 4.2 14.6 - + - -
540A ALA* 4.1 12.8 - - + +
541A GLU 3.2 13.2 - - - +
542A ALA* 3.6 12.8 - - + -
554A THR* 4.1 6.3 - - + -
555A PHE* 1.3 77.5 - - - +
557A ARG* 1.3 79.1 + - - +
558A THR* 4.3 0.2 - - + -
563A ILE* 3.7 4.7 - - - +
564A ALA* 2.9 64.7 + - + -
565A TYR* 4.0 18.2 - - - -
566A MET* 4.1 14.6 - - + -
578A VAL* 3.8 12.6 - - + -
593A VAL* 4.2 6.5 - - - -
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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