Contacts of the strand formed by residues 517 - 525 (chain B) in PDB entry 1P43
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 PRO 517 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509B SER* 4.8 8.3 - - - +
510B VAL 3.2 10.8 - - - +
511B TYR* 4.4 5.6 - - + -
512B ASP* 5.0 0.5 - - - +
515B GLY 4.4 0.9 - - - +
516B ASN* 1.3 88.8 - - + +
518B THR* 1.3 62.1 - - - +
549B ARG* 2.8 26.3 + - - -
556B TRP* 3.3 55.4 - - + +
559B LYS* 3.6 21.8 - - + +
561B VAL* 4.0 17.3 - - + +
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Residues in contact with THR 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B SER* 3.5 6.6 - - - -
510B VAL* 2.8 50.5 + - + +
512B ASP* 4.4 13.2 - - + +
517B PRO* 1.3 77.0 - - - +
519B VAL* 1.3 64.9 + - - +
533B ILE* 3.8 9.2 - - + -
534B VAL* 2.6 34.2 + - - +
535B PRO 4.4 4.5 + - - -
536B SER* 5.0 5.9 - - - -
549B ARG* 5.0 1.3 + - - +
561B VAL* 3.7 13.7 - - - -
608B ASN* 5.6 1.7 + - - +
878B THR* 4.1 11.0 - - + -
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ALA* 4.2 14.6 - - + -
508B ARG 3.9 2.7 - - - -
518B THR* 1.3 80.9 + - - +
520B GLU* 1.3 62.1 + - - +
521B VAL* 4.1 19.7 - - + -
533B ILE* 3.5 4.3 - - - +
534B VAL* 3.0 32.2 + - + +
561B VAL* 4.0 10.5 - - + -
564B ALA* 3.7 14.8 - - + -
565B VAL* 4.4 7.9 - - + -
568B VAL* 4.6 6.7 - - + -
608B ASN* 3.2 52.0 - - + +
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Residues in contact with GLU 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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414A ARG* 2.7 37.0 + - - -
506B TYR 3.9 0.3 - - - +
507B ALA* 3.1 4.0 - - - -
508B ARG* 2.6 75.3 + - + +
510B VAL* 3.5 21.7 - - + +
519B VAL* 1.3 74.5 - - - +
521B VAL* 1.3 65.3 + - - +
522B GLU* 5.4 0.2 - - - +
531B ARG* 3.5 24.4 + - + -
532B SER 3.6 5.8 - - - +
533B ILE* 3.4 20.0 - - + +
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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
----------------------------------------------------------
505B VAL* 4.7 3.6 - - + -
506B TYR 3.3 7.6 - - - +
507B ALA* 4.2 8.3 - - + -
519B VAL* 4.1 16.8 - - + -
520B GLU* 1.3 78.5 - - - +
522B GLU* 1.3 66.8 + - - +
523B LEU* 3.7 26.5 - - + -
530B PHE 3.6 0.7 - - - +
531B ARG* 3.2 4.5 - - - +
532B SER 2.9 32.3 + - - +
568B VAL* 4.4 2.9 - - + -
609B ALA 4.5 3.6 - - - +
612B GLY* 3.6 41.1 - - - +
613B VAL* 3.9 15.3 - - + +
616B ALA* 4.3 1.4 - - + +
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Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B LYS* 3.8 1.2 - - - +
505B VAL* 3.5 2.8 + - - -
506B TYR* 2.8 45.5 + - + +
508B ARG* 3.0 39.0 + - - +
520B GLU* 4.9 0.4 - - + +
521B VAL* 1.3 79.8 - - - +
523B LEU* 1.3 64.2 + - - +
524B THR* 5.0 2.2 + - - +
529B VAL* 3.7 27.7 - - + +
530B PHE 3.1 4.3 - - - -
531B ARG* 2.9 48.5 + - + +
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Residues in contact with LEU 523 (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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502B VAL* 4.0 14.8 - - + -
504B LYS 3.3 2.0 - - - -
505B VAL* 3.9 24.7 - - + -
521B VAL* 3.7 24.4 - - + -
522B GLU* 1.3 73.5 - - - +
524B THR* 1.3 60.7 + - - +
525B THR* 5.3 0.7 - - + -
528B GLY 3.6 2.1 - - - +
529B VAL* 3.5 1.7 - - - -
530B PHE* 2.9 36.1 + - + +
576B PHE* 4.2 19.3 - - + -
583B VAL* 4.6 2.9 - - + -
613B VAL* 4.0 12.6 - - + +
616B ALA* 3.9 17.0 - - + +
617B ALA* 3.7 33.9 - - + -
620B ALA* 5.1 4.7 - - + -
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Residues in contact with THR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B VAL* 3.4 5.7 - - - -
503B SER* 2.8 44.4 + - - +
504B LYS* 2.8 40.6 + - + +
522B GLU* 5.0 2.1 + - - +
523B LEU* 1.3 72.0 - - - +
525B THR* 1.3 69.2 + - - +
528B GLY 3.5 7.4 - - - +
529B VAL* 3.9 22.9 - - + +
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Residues in contact with THR 525 (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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501B ALA 3.4 18.8 - - - +
502B VAL* 4.2 17.3 - - + -
503B SER* 4.7 2.9 - - - +
523B LEU* 4.8 1.8 - - + +
524B THR* 1.3 87.4 - - - +
526B GLU* 1.3 65.7 + - - +
527B LYS* 2.9 22.6 + - - +
528B GLY* 2.9 18.2 + - - +
530B PHE* 3.4 17.4 - - + -
583B VAL* 4.9 4.7 - - + -
620B ALA* 4.0 24.9 + - + +
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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