Contacts of the strand formed by residues 329 - 333 (chain A) in PDB entry 1P22
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 VAL 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ILE* 4.8 4.3 - - + -
322A THR 3.1 11.0 - - - +
323A GLY* 4.3 1.3 - - - -
328A THR* 1.3 79.2 - - - +
330A ARG* 1.3 65.3 + - - +
342A THR* 3.5 4.7 + - - -
343A LEU* 3.1 64.3 + - + +
346A HIS* 5.2 3.6 - - + -
350A VAL* 3.7 27.4 - - + -
353A LEU* 4.5 8.7 - - + -
360A MET* 4.9 11.2 - - - -
362A THR* 3.7 14.6 - - + +
372A TRP* 5.3 7.4 - - + +
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Residues in contact with ARG 330 (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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305A GLY 2.4 31.7 + - - -
306A HIS* 2.9 47.7 - - + +
307A THR* 4.6 3.8 + - - +
321A ILE* 3.1 31.7 - - - +
322A THR* 2.8 11.5 + - - +
326A ASP* 4.1 3.6 + - - -
328A THR* 3.8 14.4 + - - +
329A VAL* 1.3 79.7 - - - +
331A VAL* 1.3 67.2 + - - +
332A TRP* 3.3 25.5 - - + +
339A MET* 4.0 16.2 - - + +
341A ASN 3.8 3.1 - - - +
342A THR* 2.7 41.4 + - - +
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Residues in contact with VAL 331 (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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319A VAL* 3.7 33.7 - - + -
320A ILE 3.4 2.5 - - - +
321A ILE* 4.4 12.3 - - + -
329A VAL* 6.2 0.2 - - + -
330A ARG* 1.3 79.7 - - - +
332A TRP* 1.3 60.7 + - - +
339A MET* 3.2 9.7 - - - +
340A LEU* 2.7 38.9 + - + -
341A ASN* 3.0 27.1 + - + +
343A LEU* 4.8 5.4 - - + -
374A MET* 5.1 0.9 - - + -
377A PRO* 3.9 10.1 - - + -
380A ILE* 3.9 26.9 - - + -
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Residues in contact with TRP 332 (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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287A ASN 6.1 0.2 - - - -
289A ILE* 3.3 26.2 - - + +
303A LEU* 3.5 17.9 - - + -
304A THR* 3.3 48.7 - - - -
305A GLY* 4.3 4.0 - - - -
306A HIS* 4.6 11.9 - + + -
319A VAL* 3.0 5.0 - - - -
320A ILE* 2.5 65.2 + - + +
322A THR* 3.1 24.8 + - + -
330A ARG* 3.3 24.6 - - + +
331A VAL* 1.3 79.6 - - - +
333A ASP* 1.3 63.4 + - - +
337A GLY 3.2 26.7 - - - +
338A GLU 3.3 5.8 - - - +
339A MET* 4.4 16.2 - - + -
340A LEU* 4.0 2.9 - - - -
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Residues in contact with ASP 333 (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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318A ARG* 3.5 35.2 + - - -
320A ILE* 4.7 2.6 - - - +
332A TRP* 1.3 71.6 - - - +
334A VAL* 1.3 62.7 - - - +
335A ASN* 2.8 18.7 + - - +
336A THR* 2.7 61.2 + - - +
337A GLY* 4.0 3.8 + - - -
338A GLU* 2.9 15.0 + - + +
340A LEU* 3.4 19.7 - - + +
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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