Contacts of the strand formed by residues 544 - 554 (chain A) in PDB entry 3M8D
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 VAL 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A GLN 3.7 0.9 - - - +
522A TYR* 3.2 13.0 - - - -
523A LEU* 2.8 50.3 + - + +
543A GLY* 1.3 90.1 - - - +
545A SER* 1.3 64.7 + - - +
546A LEU* 4.4 10.3 - - + -
571A LYS* 3.9 28.7 - - - +
572A ASP 5.2 0.2 - - - +
573A TYR* 4.0 37.9 - - + -
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Residues in contact with SER 545 (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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520A TYR* 3.1 32.0 + - - -
521A GLN 3.5 5.6 - - - -
522A TYR* 3.8 7.7 - - - +
544A VAL* 1.3 75.1 - - - +
546A LEU* 1.3 72.5 + - - +
547A TRP* 4.7 8.7 - - - -
571A LYS* 3.7 16.1 - - - +
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Residues in contact with LEU 546 (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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47A ARG* 5.8 4.9 - - - +
519A THR 3.7 0.7 - - - +
520A TYR* 3.4 5.6 - - - -
521A GLN* 3.0 43.5 + - + +
523A LEU* 4.2 17.0 - - + -
544A VAL* 4.4 6.3 - - + +
545A SER* 1.3 82.2 - - - +
547A TRP* 1.3 69.4 + - - +
548A ASP* 5.5 3.1 - - - +
567A ASN* 3.7 28.0 - - + +
571A LYS* 4.0 9.4 - - + -
573A TYR* 3.4 50.3 - - + +
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Residues in contact with TRP 547 (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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505A TYR* 5.8 6.3 - + - -
518A ILE* 3.7 31.4 - - + -
519A THR 3.2 4.3 - - - -
520A TYR* 3.4 45.3 - + + -
545A SER* 4.7 6.2 - - - -
546A LEU* 1.3 83.4 - - - +
548A ASP* 1.3 71.9 + - - +
567A ASN* 3.1 2.5 + - - +
568A LEU* 2.8 49.3 + - + +
569A PHE* 3.7 31.1 - + + +
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Residues in contact with ASP 548 (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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47A ARG* 2.8 31.3 + - - -
48A ARG* 4.7 1.5 + - - +
517A GLY 4.6 0.4 - - - -
518A ILE* 3.4 10.9 - - - +
519A THR* 2.8 43.4 + - - +
546A LEU* 5.3 3.8 - - - +
547A TRP* 1.3 78.3 + - - +
549A LEU* 1.3 61.9 + - - +
550A ALA* 6.2 0.7 - - + -
564A LYS* 4.8 12.6 - - - -
565A ILE 3.3 12.6 - - - +
566A ALA* 3.3 11.0 - - - +
567A ASN* 2.8 28.1 + - - -
568A LEU* 4.8 2.9 - - - +
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Residues in contact with LEU 549 (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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509A TRP* 5.3 0.7 - - + -
516A TRP* 3.7 36.8 - - + -
517A GLY 3.5 2.9 - - - +
518A ILE* 3.9 27.6 - - + -
548A ASP* 1.3 76.8 - - - +
550A ALA* 1.3 64.1 - - - +
551A VAL* 5.2 1.3 - - + -
564A LYS* 3.4 3.8 - - - +
565A ILE* 2.9 47.1 + - + +
568A LEU* 4.5 25.5 - - + +
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Residues in contact with ALA 550 (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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36A ARG 3.8 21.8 - - - +
37A TRP* 4.6 6.1 - - - +
38A GLN* 3.9 11.2 - - - +
515A ASP 3.6 0.7 - - - +
516A TRP* 3.4 6.6 - - - -
517A GLY* 2.8 45.4 + - - +
519A THR* 6.2 0.2 - - - +
548A ASP* 6.2 0.7 - - + -
549A LEU* 1.3 74.9 - - - +
551A VAL* 1.3 65.4 + - - +
563A GLY 3.5 3.8 - - - +
564A LYS* 4.3 9.2 - - + +
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Residues in contact with VAL 551 (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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36A ARG 6.1 0.2 - - - -
38A GLN* 3.0 9.7 + - - -
514A PHE* 5.2 8.7 - - + -
515A ASP 3.3 5.4 - - - +
516A TRP* 2.8 53.6 - - + -
549A LEU* 5.2 1.8 - - + -
550A ALA* 1.3 73.3 - - - +
552A ALA* 1.3 61.3 + - - +
561A VAL 5.7 0.2 - - - +
562A ARG* 3.2 1.0 - - - -
563A GLY* 2.8 52.0 + - - +
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Residues in contact with ALA 552 (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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36A ARG* 6.0 3.4 - - + +
38A GLN* 5.3 0.7 - - - +
513A ASP 3.9 0.7 - - - +
514A PHE* 3.6 6.1 - - - -
515A ASP* 2.9 48.4 + - + +
551A VAL* 1.3 75.0 - - - +
553A TYR* 1.3 63.3 + - - +
554A PRO* 4.6 1.1 - - - -
560A THR* 4.2 4.9 - - + -
561A VAL 3.3 6.5 - - - -
562A ARG* 3.7 34.5 - - + +
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Residues in contact with TYR 553 (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 ASP* 3.6 35.0 + - + +
514A PHE* 3.7 45.1 - + + -
552A ALA* 1.3 76.1 - - - +
554A PRO* 1.3 77.8 + - + +
555A VAL* 3.2 30.8 + - + +
560A THR* 4.0 3.8 - - - +
561A VAL* 2.7 42.3 + - + +
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Residues in contact with PRO 554 (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 ASP* 3.2 35.4 - - + +
515A ASP* 6.3 0.7 - - + -
552A ALA 4.4 1.1 - - - +
553A TYR* 1.3 91.4 - - + +
555A VAL* 1.3 65.6 + - - +
556A THR* 3.3 13.7 + - - +
557A SER* 5.8 1.1 - - - -
559A LEU 3.5 7.0 - - - +
560A THR* 4.2 10.7 - - + +
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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