Contacts of the strand formed by residues 567 - 570 (chain G) in PDB entry 6MZL
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 567 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542G HIS* 5.3 0.4 - - - -
559G LEU* 4.1 17.0 - - + -
560G SER 3.4 15.3 - - - +
561G SER* 5.1 1.8 - - - -
565G GLY 4.3 4.9 - - - +
566G THR* 1.3 79.2 + - - +
568G ARG* 1.3 65.2 + - - +
579G VAL 4.0 0.3 - - - +
580G GLY* 3.4 1.6 - - - -
581G TYR* 2.9 62.5 + - + +
582G LYS 4.3 5.4 - - - +
588G VAL* 5.2 7.6 - - + -
591G THR* 4.4 9.2 - - + -
600G PHE* 4.3 19.3 - - + -
602G SER* 5.4 3.4 - - - -
612G TRP* 5.4 5.6 - - + +
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Residues in contact with ARG 568 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541G GLY* 3.5 32.8 + - - -
542G HIS* 3.4 35.6 + - - +
558G LEU 3.5 1.2 - - - +
559G LEU* 3.5 3.2 - - - -
560G SER 2.9 33.3 + - - -
566G THR* 3.7 13.9 + - - +
567G VAL* 1.3 82.4 - - - +
569G LEU* 1.3 60.1 + - - +
570G TRP* 3.2 25.2 - - + +
577G CYS* 3.0 38.0 - - - +
579G VAL 3.2 6.7 - - - +
580G GLY* 3.7 6.9 - - - -
77K LYS* 4.0 9.1 - - - +
81K GLU* 2.7 31.5 + - - +
86K THR* 5.9 3.0 - - - +
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Residues in contact with LEU 569 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557G TYR* 4.1 19.7 - - + -
558G LEU 3.0 17.3 - - - +
559G LEU* 3.7 16.6 - - + -
568G ARG* 1.3 70.3 - - - +
570G TRP* 1.3 62.5 + - - +
577G CYS 3.8 0.3 - - - -
578G LEU* 2.9 27.0 + - + +
579G VAL* 2.9 37.3 + - + +
581G TYR* 4.8 4.4 - - - +
593G PHE* 3.7 27.8 - - + -
600G PHE* 4.7 17.7 - - + -
614G THR* 4.3 22.4 - - + +
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Residues in contact with TRP 570 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492G SER* 4.3 6.1 - - - -
539G LEU* 3.8 22.9 - - + -
540G TYR* 3.4 21.5 - - - -
541G GLY* 3.3 24.7 - - - -
542G HIS* 3.4 23.8 - + - -
556G ASN 4.0 0.3 - - - +
557G TYR* 3.6 6.6 - - - -
558G LEU* 2.9 45.7 + - + -
560G SER* 2.7 34.9 + - - -
568G ARG* 3.2 41.5 - - + +
569G LEU* 1.3 75.7 - - - +
571G SER* 1.3 66.2 + - - +
575G PHE 4.5 1.1 - - - -
576G THR* 3.2 15.5 - - - +
577G CYS* 3.2 32.5 - - + -
578G LEU* 4.0 4.6 - - - +
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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