Contacts of the strand formed by residues 320 - 324 (chain L) in PDB entry 3SWD
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 THR 320 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320J THR* 4.6 22.7 - - + -
355J HIS* 6.0 4.0 - - + -
291L ALA* 3.6 10.8 - - - +
293L ASN* 4.5 2.1 + - - +
319L GLY* 1.3 75.0 - - - -
321L GLY* 1.3 61.2 + - - +
353L ILE* 4.3 11.9 - - + -
354L CYS 3.1 15.3 - - - +
355L HIS* 3.1 33.8 + - + +
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Residues in contact with GLY 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L ALA* 3.9 7.1 - - - +
292L VAL 3.6 10.8 - - - -
293L ASN* 3.3 10.3 - - - -
314L ASN* 3.8 10.9 - - - +
320L THR* 1.3 78.6 - - - +
322L PHE* 1.3 62.5 + - - -
354L CYS* 2.8 39.5 + - - +
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Residues in contact with PHE 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346J GLU* 3.6 31.2 - - + -
348J GLU* 3.8 26.9 - - + -
353J ILE* 4.4 15.5 - - + -
355J HIS* 6.2 0.9 - + - -
292L VAL 3.7 0.3 - - - +
293L ASN* 2.7 48.3 + - + -
294L VAL 2.8 28.7 + - - -
295L ARG* 6.3 1.6 - - + -
321L GLY* 1.3 74.8 - - - +
323L ILE* 1.3 66.5 + - - +
324L THR* 3.8 19.3 - - - -
351L THR* 3.9 13.5 - - + -
352L VAL 3.4 10.3 - - - +
353L ILE* 4.5 10.3 - - + -
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Residues in contact with ILE 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294L VAL* 3.4 22.9 - - + +
296L THR* 5.0 0.2 - - + -
307L GLN* 3.5 31.0 - - + +
310L PHE* 3.5 19.1 - - + +
311L THR* 3.3 42.4 - - + +
314L ASN* 3.8 14.1 - - - +
322L PHE* 1.3 81.2 - - - +
324L THR* 1.3 66.4 + - - +
325L GLU 4.1 0.2 + - - -
332L PHE* 4.3 2.4 - - + -
350L ASN 3.9 0.9 - - - +
351L THR* 3.4 2.0 - - - -
352L VAL* 2.9 48.4 + - + +
354L CYS* 5.1 1.8 - - - -
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Residues in contact with THR 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348J GLU* 3.0 28.8 + - - +
294L VAL 2.8 13.8 + - - -
295L ARG* 3.5 21.4 - - - +
296L THR* 3.0 30.6 + - - +
322L PHE* 3.8 7.3 - - - -
323L ILE* 1.3 75.2 - - - +
325L GLU* 1.3 62.9 + - - +
326L THR* 3.9 10.3 + - + -
350L ASN* 3.5 24.2 - - - +
351L THR* 3.0 18.6 + - - +
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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