Contacts of the strand formed by residues 512 - 518 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B ALA 3.5 9.0 - - - +
504B SER* 5.0 0.2 - - - -
505B LEU* 3.8 8.1 - - - +
509B GLY 2.7 29.5 + - - +
510B GLY* 3.7 12.4 + - - +
511B LYS* 1.3 74.9 - - - +
513B LEU* 1.3 61.9 + - - +
514B LEU 4.2 7.2 - - - +
515B GLY* 5.1 0.2 - - - -
517B SER* 4.9 2.5 - - - -
527B ILE* 3.7 42.0 - - + -
529B GLY* 3.2 27.4 + - - +
585B TYR* 3.1 35.4 - - + +
589B TYR* 2.7 32.1 + - - -
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 4.3 15.3 - - + -
503B ALA* 2.9 14.8 + - + +
505B LEU* 3.7 22.7 - - + +
512B LYS* 1.3 73.9 - - - +
514B LEU* 1.3 65.7 + - + +
529B GLY* 3.0 22.9 + - - -
551B MET* 4.5 11.7 - - + -
572B VAL* 3.4 37.1 - - + +
573B VAL* 3.3 32.3 - - + -
579B PRO* 4.4 13.0 - - + -
581B ILE* 3.8 31.9 - - + -
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Residues in contact with LEU 514 (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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482B PHE* 4.5 15.0 - - + -
502B GLY* 3.2 1.7 - - - -
503B ALA* 2.6 35.2 + - - +
512B LYS* 3.5 4.7 - - - -
513B LEU* 1.3 91.8 - - + +
515B GLY* 1.3 57.8 + - - +
527B ILE 3.2 20.0 - - - +
528B TYR* 3.8 21.5 - - + -
549B LEU* 3.7 28.3 - - + +
550B THR 3.3 28.9 - - - +
551B MET* 4.5 3.4 - - + -
556B GLY* 4.2 10.3 - - - -
557B SER 3.8 4.3 - - - +
558B VAL* 4.2 13.2 - - + -
572B VAL* 4.4 3.4 - - + -
585B TYR* 4.7 0.2 + - - -
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Residues in contact with GLY 515 (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 LEU 3.3 10.3 - - - -
502B GLY* 3.8 3.6 - - - -
512B LYS* 5.1 0.4 - - - -
514B LEU* 1.3 79.4 - - - +
516B LEU* 1.3 59.5 + - - +
526B PRO* 3.5 3.1 - - - +
527B ILE* 2.7 47.4 + - - +
549B LEU* 4.5 7.2 - - - -
558B VAL* 4.3 4.7 - - - +
585B TYR* 3.8 8.3 - - - -
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Residues in contact with LEU 516 (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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499B PRO* 3.9 1.0 - - - +
500B LEU* 2.8 35.7 + - + +
501B LEU* 2.7 22.4 + - + +
515B GLY* 1.3 74.5 - - - +
517B SER* 1.3 82.5 + - - +
524B TRP* 4.0 23.8 - - + -
525B GLN 3.9 6.1 - - - +
526B PRO* 4.0 13.0 - - + -
547B VAL* 3.9 22.2 - - + -
549B LEU* 4.3 14.1 - - + +
558B VAL* 4.3 11.2 - - + -
560B ILE* 3.8 25.8 - - + -
565B LEU* 4.4 1.8 - - + -
585B TYR* 4.4 1.2 + - - -
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Residues in contact with SER 517 (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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497B ALA* 5.0 4.0 - - - +
498B SER 3.1 22.6 + - - -
499B PRO* 3.5 13.2 - - - +
500B LEU* 4.3 0.7 - - - +
512B LYS* 4.9 3.6 - - - -
515B GLY 4.2 0.2 - - - -
516B LEU* 1.3 86.1 - - - +
518B TYR* 1.4 59.5 + - - +
524B TRP* 3.6 3.0 - - - -
525B GLN* 2.7 49.0 + - - -
527B ILE* 3.5 17.9 - - - +
585B TYR* 5.2 0.2 + - - -
589B TYR* 5.0 1.7 + - - -
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Residues in contact with TYR 518 (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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490B ILE* 3.7 22.4 - - + -
492B GLU 4.2 3.1 + - - -
494B PRO* 3.3 37.6 - - + +
497B ALA* 3.7 0.8 - - - -
498B SER* 2.9 52.5 + - - -
499B PRO 3.9 5.6 - - - -
500B LEU* 3.5 34.3 - - + -
517B SER* 1.4 72.7 - - - +
519B ASP* 1.3 60.8 + - - +
523B GLN 3.4 8.1 - - - +
524B TRP* 4.1 6.7 - - + -
525B GLN* 4.2 2.2 - - - +
539B TRP* 3.6 26.2 - + + +
597B ASP 4.1 2.3 + - - -
598B SER* 3.4 26.0 - - - -
599B ARG 3.5 8.8 + - - -
600B VAL* 3.6 8.5 - - + +
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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