Contacts of the strand formed by residues 422 - 428 (chain O) in PDB entry 3H1I
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 422 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241O GLY* 4.1 9.5 - - - +
257O VAL* 4.5 7.9 - - + -
258O VAL 3.4 8.7 - - - +
259O THR* 3.3 15.0 - - - +
341O MET* 4.0 29.2 - - + +
417O PHE* 3.9 16.6 - - + +
418O VAL* 3.7 29.3 + - - +
419O SER 4.9 0.7 - - - -
420O GLY 3.9 7.0 - - - +
421O LYS* 1.3 78.7 - - - +
423O SER* 1.3 59.7 + - - +
436O LEU* 2.7 50.1 - - + +
439O LEU* 4.0 12.9 + - + +
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Residues in contact with SER 423 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU* 4.3 5.6 - - - +
166O ALA 3.8 15.0 - - - -
167O ALA* 3.4 19.3 - - - -
239O TYR* 2.6 27.4 + - - -
241O GLY* 3.1 17.0 - - - -
242O GLY 3.6 6.1 - - - -
257O VAL* 3.4 4.3 - - - +
258O VAL* 2.8 38.1 + - - -
422O LYS* 1.3 74.1 - - - +
424O MET* 1.3 61.0 + - - +
436O LEU* 4.1 0.4 - - - -
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Residues in contact with MET 424 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU* 3.6 3.8 - - - -
166O ALA* 4.0 4.0 - - - +
242O GLY 3.2 12.0 + - - +
243O GLU* 4.2 14.3 - - + +
244O ILE 3.3 22.0 + - - -
245O ARG* 5.2 6.1 - - - -
255O ALA* 5.0 2.9 - - + -
256O ALA 3.3 5.2 - - - +
257O VAL* 3.6 25.1 - - + -
337O ILE* 4.4 23.6 - - + -
423O SER* 1.3 75.0 - - - +
425O ALA* 1.3 74.0 + - - +
426O ALA* 5.1 4.5 - - + -
433O THR* 4.5 5.4 - - + -
434O PRO* 3.2 30.7 - - + +
435O PHE 5.0 0.4 - - - -
436O LEU* 3.7 34.4 - - + +
439O LEU* 5.2 3.6 - - + -
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Residues in contact with ALA 425 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 3.3 30.7 - - + +
162O ASN* 4.5 4.7 - - + -
163O LEU* 3.1 29.8 - - + +
244O ILE* 3.9 7.6 - - - -
245O ARG* 6.0 0.2 - - - -
255O ALA* 3.5 1.3 - - - +
256O ALA* 2.8 29.0 + - + +
424O MET* 1.3 78.3 - - - +
426O ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 426 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 4.0 9.2 - - - +
162O ASN* 5.1 4.3 + - - +
244O ILE 3.5 10.5 + - - +
245O ARG* 4.8 6.7 - - + +
246O GLU* 3.4 21.3 + - - +
254O HIS 3.6 14.6 - - - +
255O ALA* 4.4 4.9 - - + -
424O MET* 5.1 6.1 - - + -
425O ALA* 1.3 79.4 - - - +
427O SER* 1.3 65.9 + - - +
430O LEU* 4.0 20.2 - - + -
433O THR* 4.9 9.4 - - + -
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Residues in contact with SER 427 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O PRO* 4.7 10.0 + - - +
158O GLY* 5.7 0.4 - - - -
159O VAL* 3.1 25.6 + - - +
162O ASN* 5.5 0.9 - - - -
246O GLU* 3.8 23.3 - - - -
248O ASN* 4.4 10.4 - - - +
250O HIS* 5.4 1.4 - - - +
252O LEU 3.6 4.5 - - - +
254O HIS* 3.2 31.2 + - - +
426O ALA* 1.3 79.6 - - - +
428O GLY* 1.3 59.1 + - - +
430O LEU* 3.6 5.3 - - - +
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Residues in contact with GLY 428 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246O GLU 3.7 3.8 + - - -
247O GLN* 3.4 8.2 + - - +
248O ASN* 3.1 28.1 + - - +
250O HIS* 3.6 8.5 - - - -
252O LEU 4.2 4.0 - - - -
253O VAL* 4.2 2.0 - - - -
427O SER* 1.3 73.7 - - - +
429O ASP* 1.3 56.6 + - - -
430O LEU* 2.5 31.6 + - - +
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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