Contacts of the strand formed by residues 418 - 422 (chain A) in PDB entry 6DMY
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 LYS 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLN* 3.4 2.2 - - - +
161A THR* 2.6 63.9 + - - +
163A LYS* 4.7 32.3 - - + +
411A VAL* 5.0 12.1 - - + -
416A THR 3.6 4.9 + - - +
417A GLN* 1.3 74.0 - - - +
419A VAL* 1.3 63.8 + - - +
420A LEU* 4.2 13.4 - - + +
786A ARG* 5.9 2.7 - - - +
789A ASP* 5.5 12.0 + - + +
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 3.9 28.0 - - - -
159A ILE 3.7 7.0 - - - +
160A GLN* 4.1 15.7 - - + +
177A GLN* 4.8 9.9 - - + +
178A HIS* 4.9 2.9 - - - +
181A SER* 3.8 27.4 - - - +
407A VAL* 4.6 8.3 - - + +
410A SER* 4.5 14.1 - - - +
411A VAL* 4.3 14.9 - - + +
417A GLN 5.3 1.3 - - - +
418A LYS* 1.3 78.4 - - - +
420A LEU* 1.3 58.0 + - - +
786A ARG* 2.3 33.6 + - - +
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Residues in contact with LEU 420 (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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158A MET* 3.4 1.6 - - - +
159A ILE* 2.8 50.1 + - + +
161A THR* 3.8 31.9 - - + +
407A VAL* 5.8 2.0 - - - -
418A LYS* 4.2 10.3 - - + +
419A VAL* 1.3 80.9 - - - +
421A SER* 1.3 61.6 + - - +
786A ARG* 3.3 52.0 - - + +
789A ASP* 3.7 13.7 - - + +
790A PHE* 3.3 29.5 - - + +
793A ALA* 5.4 0.9 - - + -
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Residues in contact with SER 421 (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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157A LEU 3.3 18.6 - - - -
158A MET* 3.6 12.1 - - - -
403A TYR* 3.9 16.5 - - - -
404A VAL* 4.8 14.6 - - - +
407A VAL* 3.3 27.7 - - - +
420A LEU* 1.3 79.4 - - - +
422A PHE* 1.3 61.7 + - - +
423A THR* 5.0 0.4 - - - +
426A THR* 5.5 0.5 - - - +
786A ARG* 5.0 6.2 + - - +
787A GLU* 5.8 2.1 - - - +
790A PHE* 3.6 10.5 - - - +
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Residues in contact with PHE 422 (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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155A PRO 5.1 0.7 - - - +
157A LEU* 3.5 27.2 + - + +
404A VAL* 5.5 0.4 - - - -
421A SER* 1.3 74.4 - - - +
423A THR* 1.3 63.8 + - - +
424A THR* 4.2 11.2 + - - -
426A THR* 3.2 27.8 - - + +
427A LEU* 3.6 42.8 - - + -
430A ILE* 6.2 0.7 - - + -
777A LEU* 6.3 2.9 - - + -
787A GLU* 4.6 14.8 - - + +
790A PHE* 3.3 37.7 - + + -
791A ILE* 5.1 17.5 - - + -
794A GLN* 4.6 14.4 - - - -
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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