Contacts of the strand formed by residues 402 - 406 (chain B) in PDB entry 2Z1Z
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 PHE 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B THR* 5.7 0.7 - - - -
185B PRO* 3.7 28.7 - - + -
357B TYR* 4.1 11.4 - + - -
366B TRP* 3.2 60.8 - + + -
367B VAL 3.1 9.4 - - - +
368B HIS* 3.6 44.2 - + + -
369B PHE* 4.8 0.4 - - - -
374B SER* 2.9 9.4 - - - -
392B GLY 2.8 21.6 + - - -
398B GLY 4.1 10.1 - - - -
399B GLY 3.1 9.3 + - - -
400B GLU 3.7 18.4 - - - -
401B GLY* 1.3 79.5 - - - +
403B VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PHE* 6.3 0.4 - - + -
365B VAL 3.6 0.5 - - - +
366B TRP* 3.8 4.9 - - - -
367B VAL* 2.8 34.9 + - - +
369B PHE* 3.8 18.6 - - + -
374B SER* 4.2 10.5 - - - +
377B VAL* 3.2 37.2 - - + -
378B PHE 4.7 1.8 - - - +
381B ILE* 4.6 4.7 - - + -
389B THR* 3.6 32.5 - - + +
390B THR 3.6 11.4 - - - +
391B PRO* 4.5 0.9 - - + -
392B GLY 4.0 0.2 - - - +
402B PHE* 1.3 79.8 - - - +
404B ARG* 1.3 64.3 + - - +
405B VAL* 3.9 7.3 + - + -
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.6 5.9 - - - -
61B LEU 3.8 3.6 - - - +
62B GLY 2.8 31.9 + - - -
63B ILE* 3.8 2.0 - - - +
64B GLY 3.2 17.2 - - - +
209B ASN* 2.9 26.5 + - - +
210B PRO* 3.7 31.9 - - + +
364B TYR* 3.5 35.6 + - + -
365B VAL 3.4 8.1 - - - +
366B TRP* 4.0 15.3 - - + -
389B THR* 3.6 5.7 - - - -
390B THR* 2.9 47.7 + - - +
395B PHE* 3.3 22.1 - - + -
403B VAL* 1.3 74.0 - - - +
405B VAL* 1.3 63.0 + - - +
406B SER 4.7 1.8 - - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.7 34.1 - - + -
345B ILE* 4.0 23.1 - - + -
349B PHE* 4.1 24.0 - - + -
364B TYR* 3.6 1.9 - - - -
365B VAL* 2.8 42.4 + - + +
367B VAL* 4.5 8.5 - - + -
389B THR* 4.1 16.8 - - + -
403B VAL* 4.3 9.4 - - + -
404B ARG* 1.3 79.8 - - - +
406B SER* 1.3 65.4 + - - +
421B PHE* 4.7 6.1 - - + -
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.0 37.9 + - - +
62B GLY 3.4 24.9 + - - -
63B ILE 4.3 2.1 + - - -
64B GLY* 4.2 2.8 - - - -
345B ILE* 3.7 5.6 - - - +
363B PRO 3.8 4.9 - - - -
364B TYR* 4.0 12.8 - - - -
404B ARG* 4.1 1.6 - - - +
405B VAL* 1.3 78.4 - - - +
407B ALA* 1.3 61.5 + - - +
408B PHE* 3.3 32.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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