Contacts of the strand formed by residues 516 - 522 (chain B) in PDB entry 1DY7
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 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B GLY 4.1 4.2 - - - +
185B ALA* 5.6 0.3 - - - -
187B TYR* 2.6 41.0 + - - -
510B PHE* 3.3 9.0 - - - -
511B ASN* 3.1 47.4 + - - +
515B THR* 1.3 88.5 + - - +
517B VAL* 1.3 61.5 + - - +
518B TRP* 4.6 4.7 + - - +
533B VAL* 3.5 12.3 - - + +
534B VAL 3.2 13.2 - - - +
535B ASP* 4.7 7.1 - - - +
536B ASP 4.2 0.7 - - - +
542B LYS* 3.5 18.4 - - - -
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LYS* 5.2 0.7 - - + -
455B TYR* 3.6 39.5 - - + +
508B GLY* 4.0 10.8 - - - -
509B GLU 3.5 22.9 - - - +
510B PHE* 4.0 28.0 - - + -
516B GLU* 1.3 76.0 - - - +
518B TRP* 1.3 65.3 + - - +
519B PHE* 3.9 10.8 - - + -
532B VAL 3.8 0.7 - - - +
533B VAL* 3.7 0.3 - - - -
534B VAL* 2.9 46.5 + - + +
536B ASP* 5.1 1.3 - - + -
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Residues in contact with TRP 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PHE* 3.5 62.9 - + + -
171B VAL* 4.7 0.7 - - + -
182B ILE* 3.7 28.0 - - + -
183B ASP 4.0 2.7 - - - -
184B GLY* 4.0 9.0 + - - -
187B TYR* 3.8 21.2 - + - -
507B GLN 3.3 2.3 - - - +
508B GLY* 3.2 8.5 - - - -
509B GLU 2.8 35.4 + - - +
511B ASN* 5.0 1.6 - - - +
516B GLU* 4.6 7.0 + - - +
517B VAL* 1.3 81.1 - - - +
519B PHE* 1.3 62.1 + - - +
531B LEU* 3.8 24.5 - - + -
532B VAL 3.3 6.5 - - - +
533B VAL* 3.7 29.9 - - + +
545B ILE* 3.6 20.0 - - + -
556B LYS* 3.4 15.8 - - + -
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Residues in contact with PHE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B TYR* 3.7 31.9 - + + -
457B ASP* 5.3 3.8 - - + -
470B VAL* 3.7 31.0 - - + -
490B LEU* 5.1 0.7 - - + -
492B ILE* 4.0 27.1 - - + -
505B VAL* 4.0 18.4 - - + -
506B VAL 4.6 0.9 - - - -
507B GLN 3.9 5.4 - - - -
508B GLY* 3.4 33.7 - - - -
517B VAL* 3.9 22.9 - - + -
518B TRP* 1.3 74.3 - - - +
520B SER* 1.3 59.9 + - - +
521B VAL 3.9 0.2 + - - -
531B LEU* 3.4 4.7 - - - +
532B VAL* 2.8 34.5 + - - +
534B VAL* 4.1 15.0 - - + -
556B LYS* 3.8 7.0 - - - +
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Residues in contact with SER 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B VAL* 3.1 8.8 - - - +
506B VAL* 2.9 42.0 + - - -
519B PHE* 1.3 72.4 - - - +
521B VAL* 1.3 61.9 + - - +
522B TRP 3.6 1.3 + - - -
530B ALA 3.9 3.8 - - - -
531B LEU* 3.7 9.7 - - - +
553B PRO* 3.6 19.4 + - - +
554B THR 2.6 29.3 + - - -
556B LYS* 2.9 18.8 + - - +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 4.0 14.6 - - + -
493B ALA* 4.3 14.6 - - + -
496B ALA* 4.1 8.5 - - + -
498B ILE* 4.1 17.0 - - + -
503B PRO* 3.7 28.0 - - + -
504B ARG 4.1 1.8 - - - +
505B VAL* 4.3 6.3 - - + +
520B SER* 1.3 72.5 - - - +
522B TRP* 1.3 57.9 + - - +
523B ASN 5.4 0.2 - - - +
529B SER* 3.1 27.3 - - - -
530B ALA* 2.8 22.8 + - + +
532B VAL* 3.8 29.8 - - + -
553B PRO* 3.8 2.0 - - - +
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Residues in contact with TRP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ARG* 4.3 16.2 - - - +
175B ASP* 5.3 0.6 + - - -
443B LEU* 5.5 0.4 - - + -
459B THR* 4.3 14.1 - - + -
460B LEU* 5.3 2.9 - - + -
502B GLN 3.6 3.8 - - - +
503B PRO* 3.6 0.9 - - - +
504B ARG* 2.9 87.7 + - - +
506B VAL* 4.1 18.8 - - + -
521B VAL* 1.3 70.2 - - - +
523B ASN* 1.3 72.0 + - - +
524B GLY* 6.0 0.2 - - - -
529B SER* 4.3 1.3 - - - -
552B THR* 4.0 19.6 - - - +
553B PRO* 3.4 22.9 - - - +
554B THR* 3.6 19.9 - - + +
602B DHE 3.6 41.3 - - + -
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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