Contacts of the strand formed by residues 512 - 518 (chain A) in PDB entry 1MS4
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 LYS 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A PRO* 5.3 0.2 - - - -
503A ALA 3.5 7.4 - - - +
504A SER* 4.5 0.4 - - - +
505A LEU* 4.0 7.7 - - - +
509A GLY 2.5 36.8 + - - +
510A GLY* 3.6 12.4 + - - +
511A LYS* 1.3 76.4 - - - +
513A LEU* 1.3 60.5 - - - +
514A LEU 4.4 5.2 - - - +
515A GLY* 5.2 0.2 - - - -
517A SER* 4.7 3.6 - - - -
527A ILE* 3.4 46.0 - - + -
529A GLY* 3.0 28.7 + - - +
585A TYR* 3.3 31.9 - - + +
589A TYR* 2.8 29.9 + - - -
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Residues in contact with LEU 513 (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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482A PHE* 4.0 20.4 - - + -
503A ALA* 2.8 19.8 + - + +
505A LEU* 3.8 26.0 - - + +
512A LYS* 1.3 72.1 - - - +
514A LEU* 1.3 62.7 + - + +
529A GLY* 2.9 26.5 + - - -
551A MET* 4.3 15.3 - - + -
572A VAL* 3.5 33.3 - - + +
573A VAL* 3.6 18.4 - - + -
579A PRO* 4.8 8.1 - - + -
581A ILE* 3.9 27.6 - - + -
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Residues in contact with LEU 514 (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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482A PHE* 4.5 10.8 - - + -
502A GLY* 3.3 1.4 - - - -
503A ALA* 2.7 28.2 + - - +
512A LYS* 3.6 4.0 - - - -
513A LEU* 1.3 87.2 - - + +
515A GLY* 1.3 60.8 + - - +
527A ILE 3.4 17.5 - - - +
528A TYR* 3.9 23.8 - - + -
549A LEU* 4.0 16.5 - - + +
550A THR 3.0 36.8 - - - +
551A MET* 4.4 6.1 - - + +
556A GLY* 3.7 15.7 - - - -
557A SER 3.8 8.1 - - - +
558A VAL* 4.2 9.0 - - + -
572A VAL* 4.3 5.4 - - + -
585A TYR* 4.4 0.7 + - - -
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Residues in contact with GLY 515 (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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501A LEU 3.3 11.4 - - - -
502A GLY* 3.8 1.3 - - - -
512A LYS* 5.2 0.2 - - - -
514A LEU* 1.3 78.8 - - - +
516A LEU* 1.3 56.7 + - - +
526A PRO* 3.4 3.5 - - - +
527A ILE* 2.6 45.3 + - - +
549A LEU* 4.4 9.0 - - - -
558A VAL* 4.0 6.1 - - - +
585A TYR* 3.8 10.8 - - - -
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Residues in contact with LEU 516 (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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499A PRO* 4.1 0.7 - - - +
500A LEU* 3.0 31.3 + - + +
501A LEU* 2.8 22.0 + - + +
515A GLY* 1.3 73.4 - - - -
517A SER* 1.3 80.0 + - - +
524A TRP* 3.8 29.8 - - + -
525A GLN 3.7 1.1 - - - -
526A PRO* 3.9 19.7 - - + -
547A VAL* 4.1 19.1 - - + -
549A LEU* 4.4 12.3 - - + -
558A VAL* 4.2 12.8 - - + -
560A ILE* 3.8 25.6 - - + -
565A LEU* 4.2 2.5 - - + -
585A TYR* 4.4 2.1 + - - -
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Residues in contact with SER 517 (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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497A ALA* 4.8 2.9 - - - -
498A SER 3.1 24.2 + - - -
499A PRO* 3.6 12.5 - - - +
500A LEU 4.3 0.9 - - - +
512A LYS* 4.7 2.8 - - - -
516A LEU* 1.3 84.4 - - - +
518A TYR* 1.3 59.4 + - - +
524A TRP* 3.5 2.5 - - - -
525A GLN* 2.6 51.1 + - - -
527A ILE* 3.5 19.0 - - - +
585A TYR* 5.3 0.3 + - - -
589A TYR* 5.1 1.4 + - - -
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Residues in contact with TYR 518 (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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490A ILE* 3.8 18.4 - - + -
492A GLU 4.1 3.6 + - - -
494A PRO* 3.5 25.3 - - + +
497A ALA* 3.5 1.3 - - - -
498A SER* 2.9 53.1 + - - -
499A PRO 3.9 6.1 - - - -
500A LEU* 3.5 35.4 - - + -
517A SER* 1.3 73.9 - - - +
519A ASP* 1.3 59.3 + - - +
523A GLN 3.4 6.7 - - - +
524A TRP* 4.1 11.4 - - + -
525A GLN* 4.2 2.0 - - - +
539A TRP* 3.5 35.7 - + + +
597A ASP 4.3 1.4 + - - -
598A SER* 3.4 24.9 - - - -
599A ARG 3.5 9.7 + - - -
600A VAL* 3.6 9.9 - - + +
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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