Contacts of the helix formed by residues 556 - 567 (chain A) in PDB entry 5IY8
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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A PHE 4.5 0.2 + - - -
555A LEU* 1.3 73.5 - - - +
557A ARG* 1.3 66.1 + - - +
558A GLY* 3.1 7.0 - - - +
559A GLU* 2.9 31.5 + - + +
560A VAL 3.4 7.8 + - - -
583A ARG* 3.0 35.0 + - - +
584A PRO 4.2 2.7 - - - +
585A LEU* 3.9 12.3 - - + -
586A TRP* 4.2 2.2 - - - -
194C HIS* 5.8 2.4 + - - -
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Residues in contact with ARG 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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556A GLU* 1.3 71.7 - - - +
558A GLY* 1.3 65.7 + - - +
560A VAL* 3.6 1.6 + - - +
561A MET* 3.2 47.9 + - + +
584A PRO* 4.4 14.0 + - + +
586A TRP* 3.5 26.7 - - + -
75H TYR* 3.1 28.3 - - - +
77H PRO* 6.0 2.1 - - - +
51K LEU* 3.4 47.2 + - - +
53K ASP 4.9 3.0 + - - -
56K VAL* 4.8 11.9 + - - +
57K LEU 4.8 1.6 + - - -
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Residues in contact with GLY 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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556A GLU* 2.9 6.8 + - - +
557A ARG* 1.3 82.5 - - - +
559A GLU* 1.3 64.7 - - - -
561A MET* 3.7 3.9 + - - +
562A ASN* 3.4 14.2 + - - +
47K LYS* 3.5 15.5 + - - -
51K LEU* 4.4 22.2 - - - -
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Residues in contact with GLU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 5.0 11.4 - - + -
556A GLU* 2.9 28.3 + - + +
558A GLY* 1.3 74.7 - - - +
560A VAL* 1.3 66.4 + - - +
562A ASN* 3.0 9.3 + - - +
563A LEU* 2.9 29.5 + - + +
679A TRP* 6.0 0.4 - - + -
682A ILE* 3.4 44.5 - - + +
1035B ARG* 4.4 11.7 - - - +
47K LYS* 4.9 5.0 + - - -
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A LEU* 3.5 30.5 - - + -
556A GLU 3.4 3.5 + - - +
557A ARG 3.8 7.4 - - - +
559A GLU* 1.3 77.5 - - - +
561A MET* 1.3 60.5 + - + +
563A LEU* 3.2 9.6 + - - +
564A LEU* 2.8 45.4 + - + +
574A VAL* 5.3 0.7 - - + -
586A TRP* 3.4 49.6 - - + +
591A ILE* 3.9 18.7 - - + +
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Residues in contact with MET 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ARG* 3.2 49.6 + - + +
558A GLY 3.9 4.5 - - - +
559A GLU 3.3 0.2 - - - -
560A VAL* 1.3 80.3 - - + +
562A ASN* 1.3 57.9 + - - +
564A LEU* 3.3 8.4 + - + +
565A MET* 2.8 27.6 + - - +
574A VAL* 5.8 5.8 - - + -
75H TYR* 4.6 1.8 - - - +
51K LEU* 3.8 19.7 - - + -
56K VAL* 6.0 0.2 - - + -
57K LEU 3.1 28.7 - - - +
58K PHE* 3.4 32.9 - - + -
59K ALA 3.6 29.2 - - - +
60K GLY* 5.5 0.2 - - - -
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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 GLY 3.4 10.3 + - - +
559A GLU* 3.0 13.6 + - - +
561A MET* 1.3 75.7 - - - +
563A LEU* 1.3 59.6 + - + +
565A MET* 2.9 25.7 + - - +
566A PHE* 3.2 40.8 + - - -
678A ASN* 3.7 10.1 + - - +
47K LYS* 3.1 33.5 + - - +
60K GLY* 5.6 0.4 - - - -
61K TYR* 3.7 20.2 + - - +
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Residues in contact with LEU 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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548A PHE* 4.1 19.1 - - + -
555A LEU* 4.5 10.3 - - + -
559A GLU* 2.9 21.0 + - + +
560A VAL* 3.8 6.3 - - - +
562A ASN* 1.3 70.6 - - + +
564A LEU* 1.3 67.3 + - - +
566A PHE* 3.0 14.7 + - - +
567A LEU* 3.4 10.9 + - - +
591A ILE* 4.5 13.9 - - + -
675A VAL* 3.3 41.2 - - + +
678A ASN* 3.9 16.8 - - + +
679A TRP* 3.8 40.2 - - + +
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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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560A VAL* 2.8 39.5 + - + +
561A MET* 3.5 5.6 - - + +
563A LEU* 1.3 74.9 - - - +
565A MET* 1.3 62.9 + - - +
567A LEU* 3.3 26.1 + - + +
570A TRP* 3.5 33.9 - - + +
574A VAL* 4.0 28.5 - - + -
575A PRO* 4.6 2.5 - - + -
591A ILE* 5.0 7.6 - - + +
594A LEU* 3.5 31.4 - - + -
58K PHE* 4.1 21.8 - - + -
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Residues in contact with MET 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 MET 2.8 12.7 + - - +
562A ASN* 2.9 18.7 + - - +
564A LEU* 1.3 78.9 - - - +
566A PHE* 1.3 57.7 + - + +
567A LEU 3.6 5.9 + - - +
58K PHE* 3.9 24.7 - - - -
60K GLY* 3.9 14.6 - - - -
61K TYR 3.5 30.7 - - - +
62K LYS* 4.0 14.8 + - + +
72K ILE* 4.4 21.5 - - + -
74K ARG* 3.8 31.9 - - + +
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Residues in contact with PHE 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* 3.2 29.4 - - - -
563A LEU* 3.0 8.9 + - - +
565A MET* 1.3 75.3 - - + +
567A LEU* 1.3 61.4 + - - +
568A SER* 3.8 3.5 + - - -
674A THR* 3.4 39.7 + - + +
675A VAL* 4.4 5.2 - - + -
678A ASN* 3.0 34.3 - - + +
40K HIS* 6.4 0.9 - + - -
61K TYR* 3.8 13.9 - + - -
62K LYS* 3.7 44.9 + - + +
63K VAL* 4.6 10.3 - - + -
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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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563A LEU 3.4 2.9 + - - +
564A LEU* 3.3 27.6 + - + +
565A MET 3.8 5.2 - - - +
566A PHE* 1.3 79.3 - - - +
568A SER* 1.3 70.1 + - - +
569A THR* 3.8 3.6 - - - +
570A TRP* 3.5 40.4 - - + +
591A ILE* 5.5 4.0 - - + +
594A LEU* 4.2 32.1 - - + +
595A ILE* 4.7 11.4 - - + -
671A ASN* 3.7 26.2 - - + +
674A THR* 5.0 0.2 - - - -
675A VAL* 3.9 21.7 - - + +
62K LYS* 5.0 2.4 + - - -
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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