Contacts of the strand formed by residues 515 - 523 (chain A) in PDB entry 4QQN
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 ALA 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A THR* 3.6 20.9 - - + -
457A LEU 3.8 4.5 - - - -
458A LYS* 4.8 2.5 - - + +
513A GLY 3.6 2.4 + - - +
514A GLU* 1.3 77.2 - - - +
516A LEU* 1.3 62.5 + - - +
517A LYS* 3.5 17.8 + - - +
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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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386A ALA* 4.9 0.9 - - + -
455A PHE* 3.8 1.2 - - - +
456A THR* 3.2 2.0 - - - -
457A LEU* 2.6 61.7 + - + +
459A ILE* 3.9 25.8 - - + -
465A CYS* 4.8 8.1 - - - -
468A ILE* 5.1 0.2 - - + -
508A PHE* 3.7 34.8 - - + -
510A VAL* 4.4 3.4 - - + -
514A GLU* 3.7 16.8 + - - +
515A ALA* 1.3 70.2 - - - +
517A LYS* 1.3 65.1 + - - +
518A GLY 4.2 0.2 + - - -
538A LEU* 3.9 28.3 - - + -
539A ASN* 5.3 4.3 - - + +
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Residues in contact with LYS 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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455A PHE 3.3 5.4 - - - +
456A THR* 3.9 25.4 - - + +
515A ALA* 3.5 16.5 + - - +
516A LEU* 1.3 80.3 - - - +
518A GLY* 1.3 59.2 + - - +
538A LEU* 3.9 16.0 - - - +
539A ASN 4.8 2.4 + - - -
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Residues in contact with GLY 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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454A ASP* 3.4 7.8 - - - +
455A PHE* 2.9 46.8 + - - +
517A LYS* 1.3 75.5 - - - +
519A LYS* 1.3 60.3 + - - +
537A THR* 3.2 15.3 - - - -
538A LEU* 4.3 1.3 - - - -
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Residues in contact with LYS 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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452A SER* 4.0 27.4 + - - -
453A SER 3.5 9.9 - - - +
454A ASP* 3.5 25.5 + - - +
455A PHE* 3.4 4.2 - - - -
518A GLY* 1.3 76.3 - - - +
520A VAL* 1.3 67.2 + - - +
521A THR* 4.5 3.8 - - - +
535A THR 3.7 0.9 - - - +
536A LEU* 3.4 4.7 - - - +
537A THR* 2.8 44.3 + - + +
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Residues in contact with VAL 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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351A PHE* 5.5 0.7 - - + -
384A LEU* 4.2 5.4 - - + -
436A ILE* 3.8 31.6 - - + -
451A PHE* 4.0 3.2 - - + +
452A SER* 3.2 2.3 - - - -
453A SER* 2.8 56.1 + - - +
455A PHE* 4.0 12.8 - - + -
519A LYS* 1.3 76.3 - - - +
521A THR* 1.3 68.3 + - - +
522A VAL* 4.9 4.3 - - + -
534A VAL* 3.7 27.8 - - + -
535A THR 3.2 5.2 - - - +
536A LEU* 4.0 15.3 - - + -
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Residues in contact with THR 521 (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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451A PHE 3.2 10.1 - - - +
452A SER* 2.4 32.9 + - - +
519A LYS* 4.5 7.8 - - - +
520A VAL* 1.3 75.5 + - - +
522A VAL* 1.3 69.5 + - - +
523A HIS* 3.3 36.6 + - + +
533A THR 3.8 0.3 - - - +
534A VAL* 3.4 3.3 - - - -
535A THR* 2.8 46.0 + - - -
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Residues in contact with VAL 522 (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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351A PHE* 4.3 13.2 - - + -
353A LEU* 4.6 3.4 - - + -
449A LEU 3.9 13.0 - - - +
450A GLU* 3.3 7.6 - - - +
451A PHE* 2.9 60.7 + - + +
520A VAL* 4.9 3.8 - - + -
521A THR* 1.3 79.5 - - - +
523A HIS* 1.3 65.0 - - - +
532A LEU* 3.6 33.0 - - + -
533A THR 3.3 7.0 - - - +
534A VAL* 4.2 20.2 - - + -
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Residues in contact with HIS 523 (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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450A GLU* 3.5 17.0 - - + +
521A THR* 3.3 29.5 + - + +
522A VAL* 1.3 77.8 - - - +
524A LYS* 1.3 62.7 + - - +
525A ASN 4.0 0.2 + - - -
532A LEU* 3.1 10.4 - - - +
533A THR* 2.8 50.2 + - - +
535A THR* 4.5 13.6 + - - -
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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