Contacts of the strand formed by residues 517 - 522 (chain A) in PDB entry 1QI9
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 SER 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A PRO* 3.8 14.8 - - - -
318A PHE* 3.4 37.5 - - - -
510A LEU* 3.5 10.0 - - - +
513A PHE* 4.3 1.9 - - - -
515A GLU 3.2 11.8 + - - -
516A GLU* 1.3 78.2 - - - +
518A THR* 1.3 72.0 + - - +
533A GLN* 3.1 28.5 + - - +
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Residues in contact with THR 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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304A GLY* 5.6 2.3 - - - -
305A PRO* 5.5 2.0 - - - +
318A PHE* 4.1 10.7 - - - -
510A LEU* 3.9 7.6 - - - -
517A SER* 1.3 81.5 - - - +
519A PHE* 1.3 72.8 + - - +
520A GLU* 5.0 1.6 + - - +
530A LYS* 3.9 23.9 + - - +
531A LEU 3.3 17.5 - - - +
532A PHE* 3.9 24.9 - - + -
533A GLN 5.4 0.2 - - - +
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Residues in contact with PHE 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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318A PHE* 3.7 22.0 - + - -
322A HIS* 3.8 26.9 - + - -
431A ALA* 3.7 35.7 - - + -
432A LEU* 4.4 9.4 - - + -
506A LEU* 3.6 45.1 - - + -
509A GLU* 6.0 0.4 - - + -
510A LEU* 4.0 20.4 - - + +
513A PHE* 4.7 2.0 - + - -
518A THR* 1.3 79.2 - - - +
520A GLU* 1.3 61.1 + - - +
521A PHE* 4.7 4.0 - - + -
529A ILE 4.0 0.2 - - - +
530A LYS* 3.3 6.6 - - - +
531A LEU* 2.7 56.6 + - + +
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Residues in contact with GLU 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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431A ALA 4.6 2.5 + - - +
434A GLY* 3.5 7.3 - - - -
435A LEU* 3.0 43.0 + - + +
518A THR* 5.3 1.6 - - - +
519A PHE* 1.3 77.0 - - - +
521A PHE* 1.3 68.4 + - - +
528A VAL* 3.6 20.4 - - + +
529A ILE 3.3 13.9 - - - +
530A LYS* 3.7 33.4 + - + +
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Residues in contact with PHE 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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427A THR* 3.8 31.2 - - + -
430A LYS* 3.6 35.4 - - + +
431A ALA* 3.5 28.3 - - + -
434A GLY 4.9 0.4 - - - -
435A LEU* 4.1 17.5 - - - +
499A GLU* 5.4 0.2 - - - -
503A VAL* 4.1 12.3 - - + -
506A LEU* 4.3 5.8 - - + -
519A PHE* 4.7 6.7 - - + -
520A GLU* 1.3 84.2 - - - +
522A ARG* 1.3 70.9 + - - +
523A LEU* 3.9 18.8 - - + -
528A VAL* 3.6 1.0 - - - -
529A ILE* 2.9 53.7 + - + +
531A LEU* 5.0 6.3 - - + -
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Residues in contact with ARG 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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200A VAL* 3.9 25.1 - - - -
430A LYS* 2.9 31.9 + - + +
435A LEU* 3.9 22.3 - - + +
466A GLU* 2.7 40.1 + - - +
470A ASN* 5.3 0.3 + - - -
521A PHE* 1.3 78.6 - - - +
523A LEU* 1.3 63.2 + - - +
526A GLY 2.9 41.0 + - - +
527A GLU 3.5 4.7 - - - +
528A VAL* 3.7 17.0 - - + +
540A ASP* 5.4 0.6 + - - -
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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