Contacts of the helix formed by residues 553 - 567 (chain A) in PDB entry 2XP0
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 ASN 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A GLY* 4.0 2.3 + - - -
550A LEU 2.8 14.4 + - - +
551A ASN* 3.8 3.1 - - + +
552A ASN* 1.3 74.8 - - - +
554A SER* 1.3 58.2 + - - +
555A TYR* 3.0 12.8 + - - +
556A GLU* 2.9 35.8 + - + +
557A SER* 2.9 32.9 + - - -
644A GLN* 2.9 52.3 + - + +
650A ALA* 3.8 13.9 - - - +
655A HIS* 4.1 4.6 + - - -
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Residues in contact with SER 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLY* 4.8 7.4 - - - +
552A ASN 4.0 2.4 + - - -
553A ASN* 1.3 74.0 + - - +
555A TYR* 1.3 60.2 + - - +
557A SER* 4.2 6.1 - - - -
558A ASP* 2.8 44.6 + - - +
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Residues in contact with TYR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASN* 3.0 8.6 + - - +
554A SER* 1.3 80.1 + - - +
556A GLU* 1.3 65.9 + - - +
558A ASP* 3.4 7.6 + - + +
559A ILE* 3.2 35.6 + - + +
628A ALA* 5.0 5.5 + - - +
629A VAL* 5.9 2.0 - - + +
632A ARG* 3.6 37.7 + - - -
647A ALA 5.5 0.7 - - - +
650A ALA* 3.6 26.9 - - + -
651A MET* 3.7 44.4 + - + +
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Residues in contact with GLU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LEU* 3.5 25.8 - - + +
551A ASN* 4.7 1.3 - - - +
553A ASN* 2.9 37.9 + - + +
555A TYR* 1.3 76.1 - - + +
557A SER* 1.3 62.0 + - - +
559A ILE* 3.2 24.6 + - - +
560A LEU 3.3 8.7 + - - -
617A ARG* 4.6 4.5 + - - -
632A ARG* 2.8 31.6 + - - +
650A ALA 4.5 0.3 - - - +
653A PHE 3.7 1.2 - - - +
654A ASN* 3.7 2.6 - - - +
655A HIS* 2.9 30.4 + - + +
656A ILE* 3.5 23.2 - - + +
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Residues in contact with SER 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A LEU 3.5 19.6 - - - +
548A GLY 3.1 10.4 - - - -
549A VAL* 3.0 8.9 + - - +
550A LEU* 3.0 32.9 + - - -
553A ASN 2.9 22.5 + - - -
554A SER* 3.7 4.3 - - - -
556A GLU* 1.3 78.6 - - - +
558A ASP* 1.3 60.0 + - - +
560A LEU* 3.2 5.7 + - - +
561A LYS* 3.0 31.2 + - - +
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Residues in contact with ASP 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A SER* 2.8 30.6 + - - +
555A TYR* 3.8 7.7 - - + +
556A GLU 3.3 0.2 - - - -
557A SER* 1.3 73.3 - - - +
559A ILE* 1.3 66.9 + - - +
561A LYS* 3.3 33.0 + - - +
562A ASN* 2.9 33.9 + - - +
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Residues in contact with ILE 559 (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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555A TYR* 3.2 40.8 + - + +
556A GLU* 3.4 22.7 - - - +
557A SER 3.2 0.4 - - - -
558A ASP* 1.3 75.9 - - - +
560A LEU* 1.3 63.3 + - - +
562A ASN* 3.2 10.8 + - - +
563A TYR* 3.0 21.1 + - - +
617A ARG* 4.3 14.6 - - - +
625A LEU* 4.2 19.5 - - + +
626A PRO* 5.4 1.3 - - + -
629A VAL* 3.6 44.9 - - + -
632A ARG* 4.3 3.1 - - - +
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Residues in contact with LEU 560 (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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546A LEU* 4.6 4.7 - - + -
549A VAL* 4.1 14.4 - - + -
550A LEU* 3.9 19.3 - - + -
556A GLU 3.3 2.6 + - - -
557A SER 3.2 8.3 + - - +
559A ILE* 1.3 81.4 - - - +
561A LYS* 1.3 63.8 + - - +
563A TYR* 3.2 5.0 + - + +
564A LEU* 2.9 40.8 + - + +
574A MET* 3.9 17.3 - - + -
613A THR* 3.3 34.5 - - + +
616A TYR* 4.3 6.1 - - + -
617A ARG* 4.8 9.6 - - + +
620A ILE* 4.2 24.0 - - + -
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Residues in contact with LYS 561 (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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546A LEU* 3.8 44.6 - - + -
547A ASP* 2.6 33.4 + - - +
557A SER* 3.0 16.9 + - - +
558A ASP* 3.3 33.3 + - - +
560A LEU* 1.3 75.2 - - + +
562A ASN* 1.3 61.5 + - - +
564A LEU* 3.4 5.4 + - - +
565A ALA* 2.9 31.1 + - - +
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Residues in contact with ASN 562 (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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558A ASP* 2.9 26.7 + - - +
559A ILE* 3.5 8.3 - - - +
561A LYS* 1.3 76.5 - - - +
563A TYR* 1.3 62.0 + - - +
565A ALA* 4.0 4.9 - - - +
566A THR* 2.8 38.1 + - - +
626A PRO* 6.3 4.0 - - + +
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Residues in contact with TYR 563 (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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559A ILE 3.0 13.4 + - - +
560A LEU* 3.2 10.3 + - + +
562A ASN* 1.3 78.9 - - - +
564A LEU* 1.3 77.3 + - + +
566A THR* 4.6 0.7 - - - -
567A ARG* 3.0 83.2 + - - +
569A LEU* 4.7 3.7 - - + +
616A TYR* 4.0 22.8 + + - -
620A ILE* 3.4 51.9 - - + +
621A PRO* 5.5 1.7 - - - +
624A GLU* 3.9 6.6 - - + +
625A LEU* 3.9 19.1 - - + -
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Residues in contact with LEU 564 (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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546A LEU* 3.8 28.7 - - + -
560A LEU* 2.9 32.9 + - + +
561A LYS* 3.8 3.4 - - - +
563A TYR* 1.3 85.9 - - + +
565A ALA* 1.3 64.0 + - - +
567A ARG 3.1 2.4 + - - -
568A GLY 3.0 3.8 + - - -
569A LEU* 2.8 53.9 + - + +
570A THR 4.6 11.4 - - - +
574A MET* 4.2 20.0 - - + -
616A TYR* 3.9 31.2 - - + +
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Residues in contact with ALA 565 (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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561A LYS 2.9 18.2 + - - +
562A ASN* 4.0 5.6 - - - +
564A LEU* 1.3 77.3 - - - +
566A THR* 1.3 63.5 + - - +
568A GLY* 3.1 13.9 + - - +
569A LEU 4.3 4.0 + - - -
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Residues in contact with THR 566 (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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562A ASN* 2.8 25.2 + - - +
563A TYR* 3.7 6.1 - - - -
565A ALA* 1.3 77.7 - - - +
567A ARG* 1.3 78.8 + - + +
568A GLY 3.7 0.3 + - - -
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Residues in contact with ARG 567 (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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563A TYR* 3.0 68.1 + - - +
564A LEU 3.1 4.6 + - - +
565A ALA 3.1 0.4 - - - -
566A THR* 1.3 96.6 - - + +
568A GLY* 1.3 63.9 + - - +
569A LEU* 3.2 23.2 + - + +
624A GLU* 3.1 50.7 + - - +
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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