Contacts of the strand formed by residues 544 - 551 (chain A) in PDB entry 7EHI
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 THR 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A VAL* 6.0 1.6 - - - +
520A LEU* 3.4 25.1 - - + +
540A GLU* 3.4 2.4 - - - +
541A ASP* 2.6 48.4 + - - +
543A GLN* 1.3 88.9 - - + +
545A ARG* 1.3 65.2 + - - +
546A ILE* 5.8 0.3 - - - +
585A THR* 3.5 19.6 + - - -
586A GLU 3.7 7.9 + - - -
587A PRO* 5.1 0.9 - - - -
588A VAL* 3.7 5.2 - - - +
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Residues in contact with ARG 545 (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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520A LEU* 5.8 0.2 - - - -
538A THR* 3.4 24.5 - - + -
539A ARG 3.5 3.6 - - - -
540A GLU* 2.9 36.9 + - + -
544A THR* 1.3 79.5 + - - +
546A ILE* 1.3 58.2 + - - +
547A VAL* 3.6 17.4 + - + -
584A TRP 4.0 0.2 - - - +
585A THR* 3.4 5.4 + - - -
586A GLU* 2.6 79.1 + - + +
587A PRO 3.9 11.7 + - - -
588A VAL* 3.8 21.8 - - + +
589A ARG 4.7 5.1 + - - +
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Residues in contact with ILE 546 (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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464A MET* 4.1 7.8 - - + +
512A VAL* 4.2 3.6 - - + -
516A VAL* 4.0 21.3 - - + -
517A ILE* 3.6 31.9 - - + -
520A LEU* 4.0 15.0 - - + +
537A LEU 3.8 0.9 - - - +
538A THR* 3.4 3.6 - - - +
539A ARG* 2.9 65.0 + - + +
544A THR* 5.8 0.4 - - - +
545A ARG* 1.3 73.2 - - - +
547A VAL* 1.3 61.0 + - - +
548A GLY 4.3 0.2 - - - -
566A LEU* 4.0 7.4 - - + -
583A ILE* 3.7 24.2 - - + -
584A TRP 3.4 12.3 - - - +
585A THR* 5.1 2.0 - - - -
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Residues in contact with VAL 547 (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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464A MET* 4.3 2.9 - - - -
536A ARG* 3.5 34.5 - - + -
537A LEU 3.3 4.7 - - - +
538A THR* 4.0 4.9 - - - +
545A ARG* 3.6 30.3 - - + -
546A ILE* 1.3 79.8 - - - +
548A GLY* 1.3 63.4 + - - +
582A MET 3.8 1.2 - - - +
583A ILE* 3.2 2.8 - - - +
584A TRP* 2.9 76.4 + - + +
586A GLU* 4.4 5.4 - - - -
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Residues in contact with GLY 548 (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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464A MET* 3.9 5.3 - - - +
535A ILE 3.6 1.2 - - - +
536A ARG* 3.4 2.9 - - - +
537A LEU* 2.8 38.8 + - - -
547A VAL* 1.3 75.0 - - - +
549A VAL* 1.3 62.0 + - - -
550A PHE* 3.8 11.3 - - - -
582A MET 3.3 6.7 - - - -
583A ILE* 3.4 18.8 - - - -
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Residues in contact with VAL 549 (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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530A ILE* 4.0 15.7 - - + -
535A ILE 3.4 3.1 - - - +
536A ARG* 3.9 20.6 - - + +
548A GLY* 1.3 78.6 - - - +
550A PHE* 1.3 63.9 + - - +
551A ASN 4.2 0.2 - - - -
557A LEU* 3.8 29.4 - - + -
559A VAL* 4.4 10.8 - - + -
576A LEU* 3.6 11.1 - - + +
581A PHE* 3.1 7.1 - - - +
582A MET* 2.8 34.7 + - + +
584A TRP* 3.5 30.7 - - + -
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Residues in contact with PHE 550 (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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403A TYR* 5.3 0.4 + - + -
404A PHE* 4.4 10.8 - + + -
457A SER* 4.0 7.9 - - - -
460A THR* 4.1 3.4 - - + -
461A PHE* 3.7 61.0 - + + -
464A MET* 4.0 11.7 - - - -
533A ARG 3.9 0.2 - - - +
534A GLN* 3.4 6.1 - - - +
535A ILE* 2.9 38.9 + - + +
537A LEU* 4.2 5.4 - - + -
548A GLY* 3.8 26.0 - - - -
549A VAL* 1.3 77.7 - - - +
551A ASN* 1.3 60.3 + - - +
552A ASN* 3.5 16.0 + - - +
580A ASP 3.9 3.1 - - - -
581A PHE* 3.5 26.5 - + + -
583A ILE* 3.9 16.6 - - + -
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Residues in contact with ASN 551 (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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533A ARG 4.1 1.1 - - - -
534A GLN* 3.5 19.4 + - - +
549A VAL 4.2 0.8 - - - -
550A PHE* 1.3 69.7 - - - +
552A ASN* 1.3 56.5 + - - +
553A GLY* 3.3 12.0 + - - -
555A THR 2.8 26.4 + - - +
557A LEU* 3.7 19.9 - - + +
576A LEU* 3.0 33.9 + - + +
577A ALA 3.3 12.9 + - - +
578A PRO* 3.8 1.5 - - - -
579A ASN* 2.7 37.2 + - - -
580A ASP 3.1 13.9 + - - +
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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