Contacts of the helix formed by residues 511 - 520 (chain A) in PDB entry 4U7D
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 THR 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A LYS 3.9 1.8 + - - -
510A LEU* 1.3 77.1 - - - +
512A PRO* 1.3 68.5 - - - +
513A LEU* 4.0 9.4 + - - +
514A LYS* 2.9 48.0 + - + +
515A LEU* 3.1 8.5 + - - +
567A ILE* 4.8 9.4 - - + -
568A SER 3.9 7.4 - - - +
569A TYR* 3.3 26.6 - - + -
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Residues in contact with PRO 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A PHE* 4.0 12.1 - - + -
424A PHE* 3.7 48.9 - - + -
510A LEU 3.8 0.4 - - - -
511A THR* 1.3 88.1 - - - +
513A LEU* 1.3 61.5 + - - +
515A LEU* 3.3 4.6 + - + +
516A ILE* 3.2 28.7 + - - +
546A ILE* 5.2 0.3 - - - +
568A SER* 3.5 15.7 - - - +
570A LEU* 3.8 29.1 - - + -
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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
----------------------------------------------------------
420A PHE* 5.4 1.3 - - - -
511A THR* 4.0 8.3 - - - +
512A PRO* 1.3 80.7 - - - +
514A LYS* 1.3 71.5 + - + +
516A ILE* 3.3 6.4 + - - +
517A ASP* 3.2 41.3 + - - +
539A ARG* 4.9 8.9 + - - +
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Residues in contact with LYS 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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508A GLU* 5.5 4.4 + - - -
509A LYS 4.1 21.3 + - - +
510A LEU* 4.0 15.1 - - + +
511A THR* 2.9 29.7 + - - +
513A LEU* 1.3 89.3 - - + +
515A LEU* 1.3 62.5 + - - +
517A ASP* 3.6 5.7 + - - +
518A SER* 3.2 23.4 + - - -
527A LEU* 4.4 22.3 - - + +
569A TYR* 5.8 1.4 - - - -
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Residues in contact with LEU 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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496A LEU* 3.6 35.9 - - + +
499A ILE* 3.8 29.2 - - + -
500A LEU* 4.4 14.6 - - + -
510A LEU* 4.3 16.5 - - + +
511A THR 3.1 10.5 + - - +
512A PRO* 3.6 10.3 - - + +
513A LEU 3.3 0.2 - - - -
514A LYS* 1.3 77.2 - - - +
516A ILE* 1.3 63.6 + - + +
518A SER* 3.2 3.0 + - - -
519A TRP* 2.9 22.3 + - - +
546A ILE* 4.8 8.1 - - + -
555A LEU* 4.4 15.0 - - + -
570A LEU* 4.0 22.0 - - + -
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Residues in contact with ILE 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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420A PHE* 4.8 10.8 - - + -
512A PRO 3.2 13.2 + - - +
513A LEU* 3.3 8.3 + - - +
515A LEU* 1.3 75.1 - - - +
517A ASP* 1.3 54.0 + - - +
519A TRP* 3.1 9.2 + - + +
520A MET* 2.7 62.9 + - + +
539A ARG* 3.7 25.1 - - + +
542A LEU* 4.9 7.9 - - + -
543A GLU* 5.3 8.3 - - + +
546A ILE* 3.3 31.0 - - + -
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Residues in contact with ASP 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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513A LEU* 3.2 30.1 + - - +
514A LYS* 3.8 6.5 - - - +
516A ILE* 1.3 77.6 - - - +
518A SER* 1.3 57.0 + - - +
520A MET* 3.1 5.2 + - - +
521A GLY 2.9 4.5 + - - -
522A LYS* 2.5 44.5 + - - +
523A GLY* 3.9 25.8 + - - +
539A ARG* 3.4 25.1 + - - -
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Residues in contact with SER 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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499A ILE* 3.6 20.1 - - - +
510A LEU* 5.9 0.7 - - - -
514A LYS 3.2 15.5 + - - -
515A LEU 3.6 4.0 - - - -
517A ASP* 1.3 79.1 - - - +
519A TRP* 1.3 60.1 + - - +
521A GLY* 2.9 19.4 + - - -
522A LYS 3.6 10.0 + - - -
527A LEU* 2.7 36.0 + - - -
528A ARG* 3.4 16.0 - - - +
529A VAL 4.5 0.9 + - - -
532A VAL* 5.4 4.0 - - - +
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Residues in contact with TRP 519 (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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492A TYR* 3.7 35.9 - + + -
495A ASP* 4.5 14.0 + - + +
496A LEU* 3.8 29.4 - - + -
499A ILE* 4.1 8.9 - - + +
515A LEU 2.9 13.3 + - - +
516A ILE* 3.4 10.1 - - - +
518A SER* 1.3 76.8 + - - +
520A MET* 1.3 61.1 + - + +
521A GLY* 3.2 1.2 + - - -
532A VAL* 4.0 24.3 - - + +
533A VAL 4.4 1.6 + - - -
534A ALA* 3.1 36.4 + - + +
535A PRO* 4.2 10.7 - - + +
542A LEU* 3.7 47.8 - - + -
545A ILE* 3.9 25.4 - - + -
546A ILE* 4.1 18.4 - - + -
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Residues in contact with MET 520 (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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516A ILE* 2.7 40.0 + - + +
517A ASP* 3.5 8.5 - - - +
518A SER 3.1 0.2 - - - -
519A TRP* 1.3 77.1 - - + +
521A GLY* 1.3 60.8 + - - +
522A LYS* 3.6 21.2 + - + +
534A ALA* 4.0 10.9 - - + +
539A ARG* 3.6 32.8 - - + +
542A LEU* 3.7 28.3 - - + -
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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