Contacts of the helix formed by residues 552 - 569 (chain D) in PDB entry 1XSK
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 ASP 552 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D ALA* 3.7 11.4 - - - +
525D LYS* 2.9 24.3 + - - -
548D PRO 3.5 12.5 - - - +
549D TRP* 3.6 13.6 + - - -
551D TYR* 1.3 79.3 - - - +
553D ASP* 1.3 63.2 + - - +
554D GLU* 2.8 10.3 + - - +
555D SER* 2.5 41.9 + - - -
556D CYS 3.9 0.5 + - - -
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Residues in contact with ASP 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ARG* 5.9 0.5 + - - -
549D TRP* 5.0 9.2 - - - +
552D ASP* 1.3 73.5 - - - +
554D GLU* 1.3 65.6 + - - +
556D CYS* 3.0 24.4 + - + +
557D ASP* 3.2 15.5 + - - +
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Residues in contact with GLU 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LYS* 3.2 23.1 + - - +
552D ASP* 2.8 12.6 + - - +
553D ASP* 1.3 77.7 - - - +
555D SER* 1.3 63.3 + - - +
557D ASP* 2.8 26.8 + - + +
558D VAL* 2.9 25.7 + - + +
656D PHE* 3.2 29.9 + - - +
657D LEU* 5.6 2.5 + - + +
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Residues in contact with SER 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D ALA* 4.6 0.3 + - - +
524D TYR* 3.9 16.8 - - - -
525D LYS* 3.3 26.8 - - - +
548D PRO* 3.3 24.1 - - - +
551D TYR* 3.2 19.3 - - - +
552D ASP* 2.5 21.8 + - - -
553D ASP 3.3 0.2 - - - -
554D GLU* 1.3 71.3 - - - +
556D CYS* 1.3 60.0 + - - +
558D VAL* 3.9 1.4 - - - +
559D VAL* 3.2 29.8 + - - +
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Residues in contact with CYS 556 (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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296D ARG* 4.0 10.8 - - - -
298D LEU* 3.4 20.3 - - + +
548D PRO* 3.8 7.2 - - - -
549D TRP* 3.4 58.6 - - - -
552D ASP 3.9 0.6 + - - -
553D ASP* 3.0 14.4 + - - +
554D GLU 2.9 1.0 - - - -
555D SER* 1.3 78.5 - - - +
557D ASP* 1.3 62.1 + - - +
559D VAL* 3.5 1.8 + - - +
560D ARG* 3.0 32.2 + - - +
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Residues in contact with ASP 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ASP* 3.4 18.7 - - - +
554D GLU* 2.8 20.7 + - + +
556D CYS* 1.3 70.9 - - - +
558D VAL* 1.3 54.7 + - + +
560D ARG* 2.6 35.7 + - - +
561D PHE* 2.6 37.2 + - - +
657D LEU* 4.2 15.7 - - + -
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Residues in contact with VAL 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LYS* 3.6 31.2 - - + +
528D CYS* 3.7 25.4 - - + -
554D GLU* 2.9 21.2 + - + +
555D SER 3.9 4.7 - - - +
557D ASP* 1.3 74.5 - - - +
559D VAL* 1.3 63.1 + - - +
561D PHE* 4.4 0.4 - - - -
562D PHE* 3.1 45.4 + - + +
656D PHE* 3.3 31.9 - - + +
657D LEU* 4.0 13.7 - - + +
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Residues in contact with VAL 559 (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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271D LEU* 4.4 7.4 - - + -
298D LEU* 4.4 18.6 - - + -
524D TYR* 4.2 12.6 - - + +
528D CYS* 3.5 28.9 - - + -
532D LEU* 5.1 7.0 - - + +
539D LEU* 4.2 24.0 - - + -
548D PRO* 4.4 6.7 - - + -
555D SER 3.2 18.6 + - - +
556D CYS* 3.9 4.7 - - - +
557D ASP 3.2 0.2 - - - -
558D VAL* 1.3 79.1 - - - +
560D ARG* 1.3 62.0 + - - +
562D PHE* 4.8 1.3 - - - +
563D THR* 2.6 40.8 + - - +
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Residues in contact with ARG 560 (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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296D ARG* 2.7 34.0 + - - +
297D ASN* 3.1 32.8 - - - +
298D LEU* 3.2 27.6 - - + +
299D PRO* 4.7 2.9 - - + -
556D CYS* 3.0 15.7 + - - +
557D ASP* 2.6 39.4 + - - +
559D VAL* 1.3 74.6 - - - +
561D PHE* 1.3 66.6 + - - +
563D THR* 3.3 3.8 + - - -
564D GLN* 3.0 51.6 + - + +
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Residues in contact with PHE 561 (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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557D ASP 2.6 19.9 + - - +
558D VAL* 3.7 3.1 - - - +
560D ARG* 1.3 74.7 - - - +
562D PHE* 1.3 85.7 + + - +
564D GLN* 3.3 12.6 + - - +
565D LEU* 3.0 32.8 + - + +
639D TRP* 3.8 36.3 - + - -
657D LEU* 3.5 51.1 - - + -
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Residues in contact with PHE 562 (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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528D CYS 4.6 0.9 - - - +
529D ALA* 3.7 31.9 - - + -
532D LEU* 3.5 33.9 - - + +
533D LEU* 4.5 8.3 - - + +
558D VAL* 3.1 44.0 + - + +
559D VAL 4.8 0.2 - - - +
561D PHE* 1.3 95.2 - + - +
563D THR* 1.3 60.4 + - - +
565D LEU* 3.8 16.6 - - + +
566D LYS* 3.2 17.7 + - - +
639D TRP* 4.0 7.4 - + - -
656D PHE 3.9 9.9 - - - -
657D LEU* 3.4 26.0 - - - -
658D SER 4.1 1.8 - - - -
659D LEU* 3.7 24.7 - - + -
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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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271D LEU* 3.7 29.2 - - + +
299D PRO* 3.9 39.0 - - + +
301D HIS* 4.4 7.6 - - + -
532D LEU* 3.9 15.4 - - + +
559D VAL* 2.6 27.0 + - - +
560D ARG* 3.9 4.7 - - - -
561D PHE 3.2 0.2 - - - -
562D PHE* 1.3 76.0 - - - +
564D GLN* 1.3 65.5 + - - +
566D LYS* 3.8 2.3 + - - +
567D CYS* 3.4 23.6 + - - -
675D ASP 4.8 0.2 - - - -
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Residues in contact with GLN 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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297D ASN 5.3 0.4 + - - -
299D PRO* 5.1 3.8 - - + -
560D ARG* 3.0 43.8 + - + +
561D PHE* 3.7 13.5 - - - +
563D THR* 1.3 75.2 - - - +
565D LEU* 1.3 65.1 + - - +
567D CYS* 3.1 5.7 + - - +
568D ARG* 3.1 24.9 + - + +
675D ASP* 3.2 48.1 + - + +
676D GLN* 4.1 12.9 - - - +
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Residues in contact with LEU 565 (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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533D LEU* 4.4 7.6 - - + -
561D PHE* 3.0 23.9 + - + +
562D PHE* 3.8 23.8 - - + +
564D GLN* 1.3 74.5 - - - +
566D LYS* 1.3 63.1 + - - +
568D ARG* 2.8 24.7 + - + +
569D MET* 3.0 45.6 + - + +
638D LEU* 4.2 13.2 - - + -
639D TRP* 3.7 34.1 - - + -
661D VAL* 5.9 0.2 - - + -
671D LEU* 6.5 1.8 - - + -
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Residues in contact with LYS 566 (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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269D PHE* 2.9 35.2 + - - +
270D GLY 4.7 0.6 + - - -
532D LEU* 3.0 35.4 - - + +
533D LEU* 5.5 0.2 - - + -
534D SER 3.1 17.1 + - - +
535D SER* 3.0 25.6 + - - +
536D HIS* 3.8 3.2 - - - +
537D SER* 3.1 16.8 + - - +
562D PHE 3.2 15.1 + - - +
563D THR 4.2 4.0 - - - +
565D LEU* 1.3 78.9 - - - +
567D CYS* 1.3 63.1 + - - +
569D MET* 3.2 25.2 + - + +
570D MET* 3.3 15.2 + - - +
573D LEU* 3.7 18.8 - - + +
678D PRO* 6.5 0.2 - - + -
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Residues in contact with CYS 567 (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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270D GLY* 5.5 1.8 - - - -
301D HIS* 4.2 10.1 - - - -
563D THR* 3.4 17.4 + - - +
564D GLN 3.1 9.5 + - - +
565D LEU 3.1 0.6 - - - -
566D LYS* 1.3 80.7 - - - +
568D ARG* 1.3 55.5 + - - +
570D MET* 3.5 13.2 + - - +
674D ASN 3.7 2.0 - - - -
675D ASP* 3.8 14.1 - - - -
676D GLN 3.8 7.2 - - - -
677D ARG* 3.4 40.6 - - - +
678D PRO* 3.6 9.6 - - - -
680D TYR* 2.7 31.2 + - - -
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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
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564D GLN 3.1 18.3 + - - +
565D LEU* 2.8 14.1 + - + +
567D CYS* 1.3 76.1 - - - +
569D MET* 1.3 59.3 + - + +
570D MET 3.2 0.4 - - - -
571D PRO* 3.1 6.4 - - - +
671D LEU* 3.5 37.1 - - + +
672D GLY 2.6 50.1 + - - +
673D ASN* 5.0 2.8 - - - +
674D ASN 3.9 5.1 - - - +
675D ASP* 3.8 20.6 - - + -
680D TYR* 3.7 6.1 - - - -
687D ALA* 4.2 12.9 - - - +
689D HIS* 5.5 1.0 + - - -
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Residues in contact with MET 569 (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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532D LEU 5.5 0.2 - - - +
533D LEU* 3.6 24.7 - - + -
565D LEU* 3.0 40.8 + - + +
566D LYS* 3.2 24.8 + - + +
568D ARG* 1.3 77.5 - - + +
570D MET* 1.3 52.5 + - - +
571D PRO* 3.3 3.1 - - - -
572D TYR* 3.1 16.3 + - + +
573D LEU* 2.7 51.8 + - + +
610D LEU* 5.5 4.7 - - + -
614D VAL* 6.1 4.5 - - - -
638D LEU* 4.0 24.5 - - + -
661D VAL* 6.0 1.1 - - - -
669D LEU* 6.5 0.4 - - + -
671D LEU* 4.8 15.9 - - + -
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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