Contacts of the strand formed by residues 551 - 561 (chain A) in PDB entry 2PY5
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 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A GLY 3.2 10.4 + - - -
550A PHE* 1.3 77.9 - - - +
552A ARG* 1.3 88.4 + - - +
571A THR* 3.2 16.3 - - - +
572A PHE 3.2 4.5 - - - -
573A THR* 3.0 23.6 + - - -
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Residues in contact with ARG 552 (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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537A ILE* 4.3 13.5 - - + -
540A GLU* 3.2 31.9 + - + +
545A ASN* 3.8 14.6 - - - +
550A PHE* 3.7 45.6 - - + +
551A SER* 1.3 102.0 + - - +
553A LYS* 1.3 59.7 + - - +
554A MET* 3.1 35.0 + - + +
571A THR* 4.4 1.8 - - - -
572A PHE* 2.8 33.0 + - - +
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Residues in contact with LYS 553 (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* 1.3 68.7 - - - +
554A MET* 1.3 63.2 + - - +
568A VAL* 5.7 0.4 - - - +
569A ASP* 3.1 35.5 + - + +
570A ASP* 3.4 23.8 + - - +
571A THR* 3.9 19.3 + - + +
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Residues in contact with MET 554 (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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534A THR* 4.3 4.9 + - - -
536A LYS* 3.3 58.4 - - + +
537A ILE* 3.7 23.3 - - + +
540A GLU* 3.7 31.0 - - - +
552A ARG* 3.1 28.9 + - + -
553A LYS* 1.3 81.7 - - - +
555A LYS* 1.3 61.9 + - - +
556A PRO* 3.3 12.1 - - - +
569A ASP* 4.0 14.2 - - - +
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Residues in contact with LYS 555 (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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532A GLY* 3.3 36.7 + - - +
534A THR* 4.1 11.9 - - + -
537A ILE* 4.2 5.1 - - + +
554A MET* 1.3 77.6 - - - +
556A PRO* 1.3 80.1 - - + +
557A LYS* 6.4 0.7 - - + -
569A ASP* 4.2 0.9 - - - -
570A ASP* 2.7 45.4 + - + +
571A THR 5.5 1.3 - - - +
572A PHE* 3.9 33.1 - - + +
3J A 5.5 5.4 + - - -
5J T 5.3 8.5 - - - +
1Y G 4.7 6.9 + - - +
2Y G 5.7 7.1 - - - -
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Residues in contact with PRO 556 (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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534A THR* 4.0 17.0 - - + -
554A MET 3.3 10.3 - - - +
555A LYS* 1.3 94.9 - - + +
557A LYS* 1.3 58.5 + - - +
558A PRO* 4.4 3.4 - - - +
567A LEU* 4.0 24.2 - - + +
568A VAL 3.5 7.6 - - - +
569A ASP* 4.0 12.3 - - - +
5J T 5.0 4.2 - - - +
6J T 4.1 25.8 - - + +
7J T 4.1 17.9 - - + +
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Residues in contact with LYS 557 (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 LYS* 4.4 0.7 - - + +
556A PRO* 1.3 74.6 - - - +
558A PRO* 1.3 78.1 - - + +
559A VAL* 3.5 10.9 + - + +
566A VAL 3.4 0.7 - - - +
567A LEU* 4.1 2.2 - - - -
568A VAL* 2.8 38.2 + - + +
570A ASP* 3.6 31.9 - - + +
3Y A 4.5 27.3 + - - -
4Y C 5.5 2.2 + - - -
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Residues in contact with PRO 558 (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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64A LYS* 6.0 7.0 - - - -
556A PRO 4.4 2.7 - - - +
557A LYS* 1.3 94.3 - - + +
559A VAL* 1.3 62.4 + - - +
560A GLN 4.4 0.3 + - - -
565A VAL* 3.6 19.7 - - + -
566A VAL 3.6 5.8 - - - +
567A LEU* 3.7 15.0 - - + -
5J T 6.3 0.7 - - - +
6J T 5.4 5.4 - - - +
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Residues in contact with VAL 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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19A VAL* 5.3 3.6 - - + -
557A LYS* 3.9 12.3 - - + +
558A PRO* 1.3 78.8 - - - +
560A GLN* 1.3 74.6 + - - +
561A VAL* 3.4 15.0 + - + +
565A VAL* 3.3 6.5 - - - +
566A VAL 2.9 34.0 + - - +
568A VAL* 3.9 26.5 - - + -
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Residues in contact with GLN 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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64A LYS 5.2 1.6 - - - +
68A ALA* 3.8 12.8 - - - +
100A TRP* 5.1 2.4 - - - -
407A LYS* 5.1 6.2 + - - +
409A ASN* 5.6 0.7 + - - -
411A ALA* 3.7 11.6 - - + +
412A LEU* 3.6 46.1 - - - +
414A PHE* 3.9 10.4 - - + -
558A PRO 4.3 0.6 - - - -
559A VAL* 1.3 77.5 - - - +
561A VAL* 1.3 64.5 + - - +
564A GLY* 3.6 8.8 + - - -
565A VAL* 3.4 26.7 - - - +
5Y T 3.1 31.8 + - + +
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Residues in contact with VAL 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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19A VAL* 3.6 31.9 - - + +
22A CYS* 3.4 35.0 - - + -
72A ASN* 4.2 1.9 + - - +
411A ALA* 3.5 14.5 - - - +
412A LEU 4.6 0.7 + - - -
559A VAL* 3.9 19.5 - - + +
560A GLN* 1.3 78.3 - - - +
562A PRO* 1.3 78.6 - - + +
563A GLY 3.1 2.8 + - - -
564A GLY 2.9 26.8 + - - +
566A VAL* 3.9 10.3 - - + +
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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
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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