Contacts of the strand formed by residues 564 - 573 (chain A) in PDB entry 1XI1
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 GLY 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A CYS* 3.7 8.9 - - - -
68A ALA* 4.4 3.6 - - - -
69A PHE* 4.2 8.5 - - - -
72A ASN* 3.4 15.3 - - - -
560A GLN* 3.6 6.1 - - - +
561A VAL* 2.7 35.6 + - - +
562A PRO 3.2 2.4 + - - -
563A GLY* 1.3 78.6 - - - +
565A VAL* 1.3 65.0 + - - -
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Residues in contact with VAL 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 4.7 1.0 + - - -
16A THR 4.9 0.5 - - - +
22A CYS* 3.5 0.2 - - - -
64A LYS 4.6 6.3 - - - +
65A PHE* 3.9 32.3 - - + +
68A ALA* 3.2 28.0 - - + -
69A PHE* 3.3 26.2 - - + -
558A PRO* 3.6 31.2 - - + -
559A VAL 3.5 7.2 - - - +
560A GLN* 3.2 23.3 - - - +
564A GLY* 1.3 74.8 - - - -
566A VAL* 1.3 76.9 + - - +
567A LEU* 4.7 0.2 - - + -
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Residues in contact with VAL 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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16A THR 4.2 10.8 - - - +
17A THR* 3.3 24.2 - - - +
18A LYS 3.8 11.0 - - - +
19A VAL* 4.3 16.4 - - + -
22A CYS* 3.4 31.4 - - + -
65A PHE* 5.1 0.9 - - - -
557A LYS 3.7 0.5 - - - +
558A PRO* 3.4 1.9 - - - +
559A VAL* 2.9 34.8 + - - +
561A VAL* 4.0 12.1 - - + -
565A VAL* 1.3 79.6 - - - +
567A LEU* 1.3 78.6 + - - +
568A VAL* 4.5 3.4 - - + -
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Residues in contact with LEU 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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17A THR* 4.9 5.0 - - - +
65A PHE* 4.5 11.7 - - + -
556A PRO* 4.4 19.3 - - + -
557A LYS 3.6 3.1 - - - +
558A PRO* 3.8 28.5 - - + -
566A VAL* 1.3 86.1 - - - +
568A VAL* 1.3 61.1 + - - +
4C T 3.7 44.6 - - + +
5C T 4.0 40.6 - - + +
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Residues in contact with VAL 568 (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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19A VAL* 4.6 15.0 - - + -
556A PRO* 3.0 4.6 - - - +
557A LYS* 2.6 39.3 + - + +
559A VAL* 3.7 31.2 - - + -
566A VAL* 4.3 10.1 - - + +
567A LEU* 1.3 79.2 - - - +
569A ASP* 1.3 81.3 + - + +
570A ASP* 3.6 0.6 + - + -
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Residues in contact with ASP 569 (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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553A LYS* 3.8 29.3 - - + +
554A MET* 3.7 19.9 - - - +
555A LYS 3.6 2.7 - - - -
556A PRO* 3.8 13.2 - - - +
568A VAL* 1.3 86.4 - - - +
570A ASP* 1.3 60.6 + - - +
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Residues in contact with ASP 570 (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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552A ARG 4.0 0.5 - - - +
553A LYS* 4.3 4.0 - - - -
555A LYS* 2.7 33.1 + - - +
557A LYS* 3.7 42.6 + - + +
568A VAL* 3.6 0.6 + - + -
569A ASP* 1.3 75.6 - - - +
571A THR* 1.3 91.6 + - - +
572A PHE 3.2 3.3 + - - -
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Residues in contact with THR 571 (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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551A SER* 4.0 10.1 - - - +
552A ARG 3.6 10.1 - - - +
553A LYS* 2.8 41.7 - - + +
555A LYS* 5.6 0.2 - - - -
557A LYS* 5.1 2.4 + - - -
570A ASP* 1.3 86.5 + - - +
572A PHE* 1.3 64.2 + - - +
573A THR* 3.5 21.2 + - - +
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Residues in contact with PHE 572 (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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530A CYS* 3.6 22.9 - - - -
531A ALA* 5.1 2.9 - - + -
532A GLY* 3.1 41.7 - - - -
533A MET* 3.5 31.6 - - + -
537A ILE* 3.8 33.7 - - + -
550A PHE* 4.7 3.6 - + - -
551A SER* 2.9 23.6 - - - -
552A ARG 2.9 11.6 + - - +
555A LYS* 3.9 25.6 - - + -
557A LYS* 6.2 0.2 - - - +
570A ASP 3.2 1.6 + - - -
571A THR* 1.3 73.7 - - - +
573A THR* 1.3 69.3 + - - +
574A ILE* 4.0 14.1 - - + -
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Residues in contact with THR 573 (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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549A GLY* 3.6 20.0 - - - +
550A PHE 3.1 11.0 - - - +
551A SER* 2.9 17.5 - - - -
571A THR* 3.5 13.8 + - - +
572A PHE* 1.3 86.6 - - - +
574A ILE* 1.3 69.3 + - - +
575A LYS* 3.3 27.4 + - + +
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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