Contacts of the strand formed by residues 528 - 537 (chain A) in PDB entry 2ADS
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 LEU 528 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A LYS* 4.2 8.7 - - + -
521A ILE 3.5 19.3 - - - +
522A PHE* 3.7 35.4 - - + -
527A GLU* 1.3 78.4 - - - +
529A VAL* 1.3 63.2 + - - +
530A ARG 3.7 17.0 - - - +
531A TYR* 4.4 7.6 - - + +
701A ASP* 4.0 17.8 - - - +
702A ILE 3.2 35.7 - - - +
703A MSE 3.8 22.8 - - + -
705A TRP* 4.0 8.5 - - - +
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Residues in contact with VAL 529 (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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521A ILE* 2.9 21.1 + - + +
522A PHE 3.9 2.5 - - - +
523A ASN* 3.5 44.9 - - + +
527A GLU* 5.9 0.2 - - + -
528A LEU* 1.3 74.4 - - - +
530A ARG* 1.3 72.6 + - + +
558A LEU* 3.7 36.3 - - + -
560A PHE* 4.4 10.1 - - + -
701A ASP* 3.3 15.1 - - - +
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Residues in contact with ARG 530 (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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521A ILE* 2.9 30.9 + - + +
528A LEU* 3.7 7.1 - - - +
529A VAL* 1.3 97.9 + - + +
531A TYR* 1.3 63.6 + - - +
554A LEU* 4.6 22.5 - - + +
558A LEU* 4.4 21.0 - - + +
699A GLU* 4.0 21.2 + - + +
700A GLY* 3.2 25.0 - - - +
701A ASP* 4.0 8.6 + - - +
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Residues in contact with TYR 531 (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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447A LEU* 4.3 2.5 - - + +
450A MSE 4.1 5.6 - - + +
518A PHE* 4.3 3.4 - + + -
519A THR 3.7 4.9 - - - -
520A LYS* 4.1 19.3 - - + +
528A LEU* 4.4 8.0 - - + +
530A ARG* 1.3 76.2 - - - +
532A TYR* 1.3 65.5 + - - +
533A LEU* 3.9 8.3 - - + -
698A LYS* 3.5 51.6 + - + +
699A GLU* 3.3 23.9 - - - +
700A GLY* 2.9 51.3 + - - +
701A ASP* 3.7 4.4 - - - +
702A ILE* 3.7 19.5 - - + +
704A TYR* 3.6 44.3 - + + -
705A TRP* 5.3 0.2 - - + -
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Residues in contact with TYR 532 (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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517A ALA 3.7 6.3 - - - +
518A PHE* 4.0 0.9 - - - -
519A THR* 2.8 42.8 + - + +
521A ILE* 6.1 0.9 - - + -
531A TYR* 1.3 77.8 - - - +
533A LEU* 1.3 57.3 + - - +
534A THR* 3.1 30.3 + - + +
536A TYR* 3.3 22.1 + - - -
547A ALA 4.7 2.0 - - - -
550A ASP* 3.1 41.3 + - + -
551A VAL* 4.4 17.9 - - + -
554A LEU* 4.4 15.9 - - + -
697A LYS* 5.8 5.3 - - + -
698A LYS 4.2 1.8 - - - -
699A GLU* 3.7 27.4 - - + -
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Residues in contact with LEU 533 (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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447A LEU* 4.9 4.7 - - + -
516A VAL* 3.5 30.3 - - + -
518A PHE* 3.7 26.7 - - + -
531A TYR* 3.9 3.0 - - + -
532A TYR* 1.3 71.1 - - - +
534A THR* 1.3 60.9 + - - +
685A ILE* 3.8 24.5 - - + +
686A THR* 5.4 0.2 - - - -
689A MSE 3.9 24.5 - - + -
696A ILE* 3.9 13.6 - - + +
697A LYS* 3.7 1.9 - - - -
698A LYS* 3.0 38.4 + - + +
704A TYR* 3.6 22.9 - - + +
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Residues in contact with THR 534 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A VAL* 3.8 12.9 - - - +
517A ALA 4.1 3.4 + - - +
532A TYR* 3.1 45.8 + - - +
533A LEU* 1.3 78.3 + - - +
535A SER* 1.3 71.9 - - - +
536A TYR* 3.2 28.8 - - + -
696A ILE* 4.0 9.4 - - - +
697A LYS* 4.0 31.6 - - + +
698A LYS 4.2 1.6 + - - -
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Residues in contact with SER 535 (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 ASN* 2.9 32.1 + - - -
515A ALA 3.9 4.0 - - - -
516A VAL* 4.2 8.1 - - - +
534A THR* 1.3 86.3 - - - +
536A TYR* 1.3 64.6 + - - +
537A PRO* 3.9 6.7 - - - +
689A MSE 6.0 1.1 - - - -
695A PRO* 3.9 13.9 - - - +
696A ILE* 3.2 34.9 + - - +
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Residues in contact with TYR 536 (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 ASN* 3.4 2.7 - - - -
515A ALA* 2.8 41.5 + - + +
517A ALA* 3.6 24.0 + - + +
532A TYR* 3.3 23.2 + - - -
534A THR* 3.2 27.4 - - + -
535A SER* 1.3 78.9 + - - +
537A PRO* 1.3 70.4 - - - +
543A LEU* 3.1 27.3 - - + +
546A LYS* 4.1 20.4 - - + -
547A ALA* 3.4 34.8 - - + +
550A ASP* 3.2 26.8 + - - -
551A VAL* 5.7 0.2 - - - +
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Residues in contact with PRO 537 (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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513A VAL 4.4 2.0 - - - +
514A ASN* 3.4 16.8 - - - +
535A SER* 3.9 8.1 - - - +
536A TYR* 1.3 92.7 - - - +
538A ALA* 1.3 64.9 + - - +
539A PHE* 3.3 28.5 + - + -
543A LEU* 3.1 8.8 - - - +
546A LYS* 6.3 0.9 - - - +
695A PRO* 5.3 11.9 - - + -
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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