Contacts of the strand formed by residues 323 - 330 (chain I) in PDB entry 2B4X
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 323 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77I PHE* 6.4 0.2 - + - -
281I MET* 4.4 7.6 - - + -
320I MET* 3.8 23.1 - - + -
321I PRO* 3.4 14.8 - - + -
322I ARG* 1.3 76.7 - - - +
324I ARG* 1.3 61.5 + - - +
325I ILE* 4.0 16.8 - - + -
373I LEU* 4.2 13.9 - - + -
374I GLU* 3.4 2.4 - - - +
375I VAL* 2.7 64.7 + - + +
408I PHE* 4.0 6.3 - + - -
410I VAL* 4.3 13.7 - - + -
426I VAL* 3.4 40.4 - - + -
429I PRO* 4.1 22.9 - - + -
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Residues in contact with ARG 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ASN* 4.9 4.7 + - - -
323I PHE* 1.3 75.0 - - - +
325I ILE* 1.3 74.8 + - - +
326I GLU* 5.7 4.6 + - - +
372I PHE* 3.5 35.7 - - + -
373I LEU 3.3 4.0 - - - -
374I GLU* 3.0 46.3 + - + +
429I PRO 5.5 0.8 + - - -
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Residues in contact with ILE 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ASN* 3.8 26.0 - - + +
76I ILE 3.7 11.4 - - - +
77I PHE* 3.4 31.6 - - + +
323I PHE* 4.0 13.0 - - + -
324I ARG* 1.3 86.8 - - - +
326I GLU* 1.3 68.2 + - - +
327I ASP* 5.0 0.9 - - + -
371I ALA 3.7 0.9 - - - +
372I PHE* 3.5 5.8 - - - -
373I LEU* 2.7 41.9 + - + +
410I VAL* 6.0 0.4 - - + -
425I ARG 3.7 23.3 - - - +
426I VAL* 3.8 22.0 - - + -
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Residues in contact with GLU 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I ARG 3.8 18.2 - - - +
199I THR* 4.5 9.5 + - - +
200I ASP* 4.8 4.6 - - - +
324I ARG* 5.4 6.0 + - - +
325I ILE* 1.3 79.0 - - - +
327I ASP* 1.3 65.9 + - - +
370I LYS* 3.4 38.9 + - + +
371I ALA 3.3 7.9 - - - +
372I PHE* 4.0 19.8 - - + +
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Residues in contact with ASP 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I LYS* 5.2 5.7 - - - +
75I ASN 4.6 2.8 - - - +
76I ILE* 4.1 8.5 - - - +
77I PHE* 3.4 33.8 + - + +
325I ILE* 5.0 1.3 - - + -
326I GLU* 1.3 79.9 - - - +
328I GLY* 1.3 85.2 + - - +
329I PHE* 3.5 26.6 - - + -
369I HIS 3.6 0.7 - - - +
370I LYS* 3.1 13.4 - - - +
371I ALA 3.0 31.3 + - - +
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Residues in contact with GLY 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I PRO* 6.5 0.4 - - - -
327I ASP* 1.3 88.6 + - - +
329I PHE* 1.3 66.9 + - - -
369I HIS 3.3 4.9 - - - -
370I LYS* 3.9 16.6 - - - +
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Residues in contact with PHE 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I PHE* 4.8 8.7 - + - -
66I LEU* 3.2 49.6 - - + -
70I LYS* 6.2 0.4 - - + -
76I ILE* 4.9 0.4 - - + -
77I PHE 3.7 14.1 - - - -
78I LEU* 4.0 14.6 - - + -
83I ILE* 6.1 0.2 - - + -
203I PRO* 5.6 0.8 - - - +
327I ASP* 3.5 33.9 - - + -
328I GLY* 1.3 79.9 - - - -
330I SER* 1.3 59.8 + - - +
331I LEU* 3.6 26.0 - - + -
334I GLN* 5.9 0.7 - - - -
368I PHE* 3.1 32.3 - - - +
369I HIS* 2.8 29.9 + + + +
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Residues in contact with SER 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329I PHE* 1.3 74.0 - - - +
331I LEU* 1.3 55.6 + - - +
332I LYS* 2.8 16.1 + - - +
333I GLU* 3.5 13.3 + - - +
334I GLN* 4.6 2.3 + - - +
366I ASP* 3.0 24.6 + - - -
367I ALA 3.3 6.3 - - - -
368I PHE* 3.8 12.9 - - - -
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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