Contacts of the strand formed by residues 4104 - 4108 (chain K) in PDB entry 2ZLE
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 GLY4104 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4064K ILE 3.3 0.5 - - - +
4065K GLN* 3.1 8.5 - - - +
4066K THR* 2.8 53.5 + - - +
4068K ALA 5.3 0.2 - - - -
4069K ALA* 3.9 12.2 - - - +
4090K ASN* 4.9 4.9 - - - -
4100K ASN* 5.5 1.3 - - - -
4103K ILE* 1.3 72.0 - - - +
4105K PHE* 1.3 65.7 + - - -
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Residues in contact with PHE4105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4063K PHE* 4.1 25.1 - + + -
4064K ILE 3.2 3.4 - - - -
4065K GLN* 4.1 18.8 - - + -
4090K ASN* 3.7 3.2 - - - +
4091K THR* 2.7 50.8 + - + +
4093K ILE* 3.6 44.4 - - + -
4101K ILE* 3.7 10.3 - - + -
4103K ILE* 3.4 31.0 - - + -
4104K GLY* 1.3 76.3 - - - -
4106K ALA* 1.3 61.6 + - - +
4836M PHE* 5.8 0.4 - + - -
4838M LEU* 3.9 29.2 - - + -
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Residues in contact with ALA4106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4063K PHE* 3.5 8.3 - - - -
4064K ILE* 2.7 51.8 + - + +
4066K THR* 5.7 0.7 - - + -
4079K LEU* 4.3 9.6 - - + -
4088K GLY* 4.3 4.7 - - - -
4089K ILE 3.3 21.3 - - - +
4090K ASN* 3.8 14.1 - - - +
4104K GLY 4.2 0.2 - - - -
4105K PHE* 1.3 75.5 - - - +
4107K ILE* 1.3 67.7 + - - +
4108K PRO 3.5 0.5 - - - -
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Residues in contact with ILE4107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4007K SER* 3.2 36.6 - - - +
4009K ILE* 3.7 26.9 - - + -
4063K PHE* 3.6 29.4 - - + -
4088K GLY* 2.8 24.0 - - - -
4089K ILE 2.9 16.8 + - - +
4091K THR* 4.7 5.6 - - + -
4105K PHE 4.3 0.2 + - - -
4106K ALA* 1.3 71.9 - - - +
4108K PRO* 1.3 74.8 - - + +
4111K MET* 3.7 28.5 - - + -
4112K VAL* 3.8 8.0 - - + +
4115K LEU* 4.7 1.6 - - + -
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Residues in contact with PRO4108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4028K SER* 3.4 20.9 - - - +
4062K ASN* 3.1 48.2 - - + +
4063K PHE* 4.5 0.9 - - - -
4064K ILE* 4.2 10.8 - - + +
4087K ILE 3.5 5.8 - - - +
4106K ALA 3.6 2.7 - - - +
4107K ILE* 1.3 89.6 - - + +
4109K SER* 1.3 69.2 + - - +
4110K ASN* 3.2 0.9 - - + +
4111K MET* 2.9 28.9 + - + +
4112K VAL* 2.9 12.6 + - - +
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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