Contacts of the helix formed by residues 555 - 565 (chain A) in PDB entry 3U0Z
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 VAL 555 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A GLY 5.3 2.5 - - - +
499A LYS* 2.9 39.8 + - + +
532A LEU* 4.0 30.1 - - + +
554A SER* 1.3 71.9 - - - +
556A ASP* 1.3 79.7 - - - +
558A PHE* 3.1 8.7 + - + +
559A ASN* 3.0 37.7 + - - +
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Residues in contact with ASP 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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554A SER* 3.3 5.8 + - - +
555A VAL* 1.3 89.8 - - - +
557A ASN* 1.3 62.7 + - - +
559A ASN* 3.3 5.7 + - - +
560A GLU* 2.8 31.6 + - - +
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Residues in contact with ASN 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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479A LYS* 3.3 39.1 + - + +
481A ARG* 4.0 16.2 - - - +
553A LEU* 3.6 17.0 - - + -
554A SER* 3.0 26.7 + - - +
556A ASP* 1.3 78.3 - - - +
558A PHE* 1.3 65.1 + - - +
560A GLU* 3.8 12.1 - - - +
561A VAL* 3.1 30.5 + - - +
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Residues in contact with PHE 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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476A MET* 5.2 3.0 - - + +
501A MET* 3.8 31.0 - - - -
529A GLU* 4.7 3.4 - - + -
532A LEU* 3.9 33.2 - - + -
533A LEU* 4.1 27.1 - - + -
553A LEU* 3.9 20.5 - - + +
554A SER 2.9 11.9 + - - +
555A VAL* 3.4 11.0 - - - +
557A ASN* 1.3 74.5 - - - +
559A ASN* 1.3 71.1 + - - +
561A VAL* 4.0 3.0 - - - +
562A LEU* 3.1 59.8 + - + +
569A ARG* 5.0 1.8 - - - -
572A PHE* 4.2 24.0 - + - -
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Residues in contact with ASN 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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532A LEU 5.2 4.5 + - - +
535A LYS* 4.8 14.7 + - - +
555A VAL* 3.0 35.6 + - - +
556A ASP* 3.7 8.6 - - - +
558A PHE* 1.3 84.5 - - - +
560A GLU* 1.3 60.9 + - - +
561A VAL 3.3 0.2 - - - -
562A LEU* 4.1 4.0 - - - +
563A GLU* 2.8 35.2 + - + +
569A ARG* 3.7 22.9 + - - -
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Residues in contact with GLU 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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479A LYS* 3.9 24.7 - - - -
556A ASP* 2.8 21.8 + - - +
557A ASN* 3.8 14.3 - - - +
559A ASN* 1.3 74.3 - - - +
561A VAL* 1.3 66.7 + - + +
563A GLU* 3.1 19.0 + - - +
564A GLU* 3.3 22.0 + - + +
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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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472A PHE* 3.9 28.7 - - + -
475A ALA* 4.1 28.9 - - + +
476A MET* 4.1 22.2 - - - -
479A LYS* 4.7 13.5 - - + -
553A LEU* 5.8 0.4 - - + -
557A ASN 3.1 16.8 + - - +
558A PHE 4.0 3.1 - - - +
560A GLU* 1.3 77.8 - - + +
562A LEU* 1.3 59.1 + - + +
564A GLU* 3.0 11.6 + - - +
565A TYR* 3.0 35.7 + - + +
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Residues in contact with LEU 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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472A PHE* 4.1 15.3 - - + -
476A MET* 5.7 2.0 - - + -
533A LEU* 4.7 0.9 - - + -
558A PHE* 3.1 55.6 + - + +
559A ASN* 4.1 5.8 - - - +
560A GLU 3.3 0.2 - - - -
561A VAL* 1.3 75.5 - - + +
563A GLU* 1.3 66.8 + - - +
565A TYR 3.5 14.7 - - - +
566A PRO* 3.5 22.3 - - - +
568A MET* 4.1 17.9 - - + +
569A ARG* 4.0 43.6 - - + +
572A PHE* 4.2 10.1 - - + -
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Residues in contact with GLU 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 ASN* 2.8 19.8 + - + +
560A GLU* 3.2 14.6 - - - +
562A LEU* 1.3 74.4 - - - +
564A GLU* 1.3 63.4 + - + +
566A PRO* 3.9 11.6 - - - +
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Residues in contact with GLU 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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475A ALA* 4.6 8.2 - - - +
560A GLU* 3.7 27.5 - - + +
561A VAL* 3.0 10.9 + - - +
563A GLU* 1.3 77.5 - - + +
565A TYR* 1.3 88.8 + - + +
566A PRO* 3.3 7.8 - - - +
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Residues in contact with TYR 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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469A ASP* 3.8 20.2 - - + -
471A ASN* 3.4 25.5 + - + +
472A PHE* 3.7 52.9 - + + -
475A ALA* 4.3 9.2 - - + +
561A VAL* 3.0 19.7 + - + +
562A LEU* 3.5 8.8 - - - +
563A GLU 3.3 0.4 - - - -
564A GLU* 1.3 107.0 + - + +
566A PRO* 1.3 66.4 - - - +
567A MET* 3.2 4.5 - - + -
568A MET* 2.9 20.5 + - + +
569A ARG 3.6 2.1 + - - -
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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