Contacts of the helix formed by residues 557 - 573 (chain D) in PDB entry 2QLF
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 GLU 557 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D LEU* 1.3 74.0 - - - +
558D ILE* 1.3 88.5 + - - +
559D MET* 2.7 38.0 + - - +
560D GLN* 2.8 36.3 + - + +
561D ILE* 2.9 10.4 + - - +
595D LEU* 5.1 0.3 - - - +
597D LYS 4.3 2.3 - - - +
598D GLU* 3.5 29.5 - - + -
599D LEU 2.9 37.6 + - - +
600D TYR* 3.3 18.9 - - + +
812G HIS* 4.7 6.5 + - - +
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Residues in contact with ILE 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C LEU* 5.0 2.2 - - + -
482C PHE* 4.6 13.2 - - + -
520D LEU* 4.0 25.4 - - + -
549D LEU* 5.6 1.3 - - + -
556D LEU 3.7 0.8 + - - -
557D GLU* 1.3 90.2 - - - +
559D MET* 1.3 64.3 + - + +
561D ILE* 3.3 14.6 + - + +
562D LEU* 2.9 51.9 + - + +
595D LEU* 4.1 5.6 - - + -
599D LEU* 2.9 35.4 + - + +
601D PHE* 3.9 31.4 - - + -
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Residues in contact with MET 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B MET* 3.8 57.0 - - + -
263B THR* 5.1 5.8 - - - +
293B SER* 4.5 8.1 - - - -
520D LEU* 4.1 17.3 - - - -
557D GLU* 2.7 25.8 + - - +
558D ILE* 1.3 81.6 - - + +
560D GLN* 1.3 55.3 + - + +
562D LEU* 3.8 2.0 - - + -
563D THR* 2.8 39.9 + - - +
591D VAL* 3.5 40.2 - - + -
593D SER* 4.4 8.3 - - - +
595D LEU* 6.0 0.9 - - + -
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Residues in contact with GLN 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.4 34.3 + - + +
555D ASP 4.9 0.2 - - - +
556D LEU* 3.6 27.4 - - + +
557D GLU* 2.8 40.0 + - + +
559D MET* 1.3 74.6 - - + +
561D ILE* 1.3 67.4 + - - +
563D THR* 3.4 5.2 + - - -
564D ARG* 3.0 34.7 + - - +
600D TYR* 4.2 6.1 + - - -
812G HIS* 3.4 40.9 + - + +
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Residues in contact with ILE 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D LEU* 4.7 4.0 - - + -
548D ILE* 3.9 21.3 - - + +
549D LEU* 3.9 36.1 - - + -
552D HIS* 4.1 4.5 - - + +
553D GLY* 4.0 18.4 - - - +
556D LEU* 3.5 33.4 - - + +
557D GLU 2.9 14.6 + - - +
558D ILE* 3.5 21.1 - - + +
560D GLN* 1.3 75.2 - - - +
562D LEU* 1.3 65.9 + - + +
564D ARG* 3.0 8.6 + - - +
565D VAL* 3.0 28.9 + - + +
601D PHE* 4.5 4.9 - - + -
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Residues in contact with LEU 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C PHE* 4.1 15.0 - - + -
520D LEU* 3.8 30.3 - - + -
522D ALA* 4.0 22.7 - - + -
541D PHE* 4.9 6.7 - - + -
545D LEU* 4.2 17.3 - - + -
558D ILE* 2.9 38.6 + - + +
559D MET* 4.2 4.9 - - + +
561D ILE* 1.3 75.6 - - + +
563D THR* 1.3 56.4 + - - +
565D VAL* 3.0 10.3 + - + +
566D ASN* 2.9 33.1 + - - +
591D VAL* 3.8 26.2 - - + -
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Residues in contact with THR 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B MET* 5.1 5.4 - - - +
293B SER* 4.8 6.6 + - - -
295B LEU* 4.0 8.3 + - - +
296B THR 3.6 2.5 - - - +
297B LYS* 3.5 43.3 + - - +
298B GLU* 4.5 5.2 - - + +
559D MET* 2.8 33.9 + - - +
560D GLN* 3.7 6.1 - - - -
561D ILE 3.2 0.2 - - - -
562D LEU* 1.3 75.4 - - - +
564D ARG* 1.3 66.2 + - + +
566D ASN* 3.1 20.7 + - - +
567D ASP* 3.1 13.0 + - - +
591D VAL* 5.3 0.2 - - - +
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Residues in contact with ARG 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TYR* 3.3 68.8 + - + +
296B THR 5.3 0.4 - - - -
298B GLU* 4.5 11.1 + - - -
548D ILE* 4.2 21.6 - - + +
552D HIS* 3.3 34.9 + - - -
556D LEU* 3.5 28.2 - - - +
560D GLN* 3.0 22.0 + - - +
561D ILE 3.4 7.4 - - - +
563D THR* 1.3 80.5 - - + +
565D VAL* 1.3 57.2 + - - +
567D ASP* 3.6 7.2 + - - +
568D ARG* 3.0 28.8 + - - +
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Residues in contact with VAL 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D PHE* 3.9 29.2 - - + -
544D ALA* 3.7 19.7 - - + -
545D LEU* 3.8 28.9 - - + +
548D ILE* 3.7 21.8 - - + -
561D ILE* 3.0 20.8 + - + +
562D LEU* 3.0 16.4 + - + +
564D ARG* 1.3 75.4 - - - +
566D ASN* 1.3 66.0 + - - +
568D ARG* 3.6 5.2 - - - +
569D VAL* 2.9 24.5 + - + +
589D PRO* 4.8 0.2 - - + -
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Residues in contact with ASN 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B SER* 3.8 20.6 + - - -
294B MET* 5.0 0.2 - - - -
295B LEU 3.2 24.0 + - - +
562D LEU 2.9 18.7 + - - +
563D THR* 3.3 12.6 + - - +
565D VAL* 1.3 79.0 - - - +
567D ASP* 1.3 58.2 + - - +
569D VAL* 3.2 2.3 + - - +
570D ALA* 2.9 30.1 + - - +
588D ILE* 3.8 14.5 - - + +
589D PRO* 2.8 46.7 - - - +
590D CYS 4.1 0.7 + - - -
591D VAL* 4.0 11.7 - - - +
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Residues in contact with ASP 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B THR* 3.2 45.4 - - - +
297B LYS* 3.2 19.6 + - - -
563D THR 3.1 7.1 + - - +
564D ARG* 3.9 6.7 - - - +
566D ASN* 1.3 78.9 - - - +
568D ARG* 1.3 52.9 + - - +
570D ALA* 3.7 0.8 - - - -
571D ARG* 2.7 70.4 + - - +
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Residues in contact with ARG 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D ALA* 4.3 12.3 - - + +
547D SER* 3.1 29.3 + - - -
548D ILE* 4.4 14.2 - - + +
551D GLU* 5.4 1.2 + - - -
564D ARG 3.0 18.8 + - - +
565D VAL* 3.6 7.6 - - - +
567D ASP* 1.3 74.9 - - - +
569D VAL* 1.3 60.8 + - - +
571D ARG* 5.1 0.9 - - - -
572D HIS* 2.8 76.9 + - + +
573D PHE* 3.9 11.0 - - - -
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Residues in contact with VAL 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D TRP* 4.2 9.5 - - + +
541D PHE* 3.8 16.8 - - - +
544D ALA* 3.5 21.5 - - + -
565D VAL* 2.9 22.1 + - + +
566D ASN 3.6 3.1 - - - +
568D ARG* 1.3 76.2 - - - +
570D ALA* 1.3 62.8 + - - +
573D PHE* 3.2 31.1 + - - +
587D GLN* 3.5 39.4 + - + +
589D PRO* 3.7 27.1 - - + -
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Residues in contact with ALA 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B LYS 3.7 3.3 - - - +
213B ILE* 5.7 0.7 - - + -
214B PRO* 3.4 28.5 - - + +
217B ALA* 5.0 0.2 - - + -
296B THR* 4.5 5.8 - - + -
566D ASN 2.9 17.1 + - - +
567D ASP* 3.7 7.0 - - - +
569D VAL* 1.3 78.4 - - - +
571D ARG* 1.3 56.5 + - + +
586D LYS* 2.7 36.8 + - - +
587D GLN 3.4 11.7 - - - +
588D ILE* 4.0 9.9 - - + -
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Residues in contact with ARG 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 3.3 33.8 + - - +
212B LYS 4.9 2.0 - - - -
213B ILE* 3.1 34.8 - - + +
218B ASP* 5.6 0.6 + - - -
296B THR* 4.5 10.7 + - - +
297B LYS* 4.5 13.4 - - - +
567D ASP* 2.7 48.6 + - - +
568D ARG* 5.1 1.3 - - - -
570D ALA* 1.3 78.1 - - + +
572D HIS* 1.3 58.9 + - - +
573D PHE 3.6 0.6 + - - -
586D LYS* 4.2 7.2 + - - +
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Residues in contact with HIS 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543D GLN* 5.7 0.8 + - - -
568D ARG* 2.8 56.9 + - + +
571D ARG* 1.3 73.4 - - + +
573D PHE* 1.3 87.2 + + + +
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Residues in contact with PHE 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D TRP* 3.3 75.6 - + + -
543D GLN* 3.7 29.4 - - + -
544D ALA* 4.6 2.9 - - + -
568D ARG* 3.6 17.5 - - - -
569D VAL* 3.2 31.5 + - - +
571D ARG 3.6 1.0 + - - -
572D HIS* 1.3 107.7 - + + +
574D GLU* 1.3 61.1 + - - +
585D LYS 4.5 0.7 - - - +
586D LYS* 3.0 28.5 + - - +
587D GLN 5.2 0.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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