Contacts of the strand formed by residues 550 - 556 (chain A) in PDB entry 3GVJ
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 GLU 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A SER* 3.6 22.6 + - - -
541A TYR* 2.7 32.0 + - + +
542A HIS* 3.2 4.5 - - - +
543A GLN* 2.8 40.5 + - + +
548A PRO* 4.0 10.7 - - + +
549A ARG* 1.3 78.2 - - - +
551A VAL* 1.3 68.7 + - - +
568A ARG* 2.9 22.6 + - - -
570A GLN* 3.6 22.3 + - - +
576A GLU* 3.3 4.5 - - - -
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Residues in contact with VAL 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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541A TYR* 3.7 15.0 - - - +
542A HIS* 4.1 4.0 - - + -
549A ARG* 5.6 0.4 - - + -
550A GLU* 1.3 80.9 - - - +
552A GLY* 1.3 61.6 + - - +
570A GLN* 3.5 3.6 - - - -
571A ILE* 3.1 45.1 + - + +
576A GLU* 3.0 20.6 + - + +
579A ALA* 3.6 39.9 - - + +
580A SER 5.1 0.7 - - - -
582A PRO* 4.0 21.8 - - + -
595A THR* 4.0 12.3 - - + -
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Residues in contact with GLY 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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540A GLY* 3.6 3.5 - - - -
541A TYR* 3.1 35.4 + - - +
551A VAL* 1.3 78.3 - - - +
553A LEU* 1.3 63.7 + - - +
569A ARG 3.2 12.1 - - - -
570A GLN* 4.0 2.0 - - - -
571A ILE* 4.2 3.4 - - - -
582A PRO* 3.6 7.4 - - - +
593A LEU* 4.2 11.9 - - - +
617A TRP* 5.8 0.4 - - - -
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Residues in contact with LEU 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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538A ALA* 4.1 13.0 - - + -
539A MET 3.2 16.4 - - - +
540A GLY* 4.4 1.6 - - - -
541A TYR* 3.5 7.1 - - - -
552A GLY* 1.3 74.3 - - - +
554A PHE* 1.3 65.4 + - - +
555A TYR* 3.9 17.0 - - + +
568A ARG* 3.7 2.8 - - - -
569A ARG* 2.9 52.0 + - + +
584A ILE* 4.4 16.2 - - + -
591A LEU* 3.2 33.9 - - + -
593A LEU* 4.7 1.1 - - + -
613A ILE 4.0 11.9 - - - +
617A TRP* 4.2 18.2 - - + -
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Residues in contact with PHE 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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402A MET* 5.3 3.6 - - + -
520A ILE* 3.9 12.6 - - + -
523A VAL* 3.7 26.7 - - + -
526A VAL* 4.5 15.3 - - + -
538A ALA* 3.2 1.9 - - - -
539A MET* 2.7 38.2 + - + +
540A GLY 5.0 0.7 - - - -
541A TYR* 3.6 35.9 - + + -
553A LEU* 1.3 75.4 - - - +
555A TYR* 1.3 58.3 + - - +
556A PHE* 3.8 21.1 - + + -
566A TYR* 3.5 31.6 - + + -
567A VAL 3.4 2.0 - - - -
568A ARG* 3.8 46.2 - - + -
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Residues in contact with TYR 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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532A ILE* 3.8 30.1 - - + +
533A ASP* 4.4 8.5 + - - -
536A GLY 4.7 0.4 - - - -
537A PHE 3.4 15.0 - - - -
538A ALA* 4.2 2.2 - - + +
553A LEU* 3.9 14.7 - - + +
554A PHE* 1.3 70.6 - - - +
556A PHE* 1.3 79.7 + - - +
557A PRO* 3.3 37.4 + - + +
566A TYR* 3.2 3.5 - - - -
567A VAL* 2.9 46.1 + - + +
569A ARG* 4.2 14.8 - - - +
613A ILE* 3.7 36.6 - - + +
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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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402A MET* 4.0 22.4 - - + -
418A LEU* 4.5 11.7 - - + -
517A LEU* 4.3 7.2 - - + -
520A ILE* 6.0 0.2 - - + -
536A GLY* 3.3 3.1 - - - -
537A PHE* 2.9 57.0 + + + +
539A MET* 4.1 17.3 - - - -
554A PHE* 3.8 22.7 - - + -
555A TYR* 1.3 75.4 - - - +
557A PRO* 1.3 67.4 - - - +
558A ASP 3.4 2.2 + - - -
559A ALA* 4.3 8.6 + - + -
563A PRO* 3.5 28.0 - - + -
565A ASN 3.7 13.0 - - - +
566A TYR* 3.7 29.8 - + + -
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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