Contacts of the strand formed by residues 307 - 311 (chain H) in PDB entry 3SZ9
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 ARG 307 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H LYS* 3.0 34.9 + - + +
273H SER 3.2 6.3 + - - +
274H PRO* 3.3 15.7 - - + +
275H ASN 2.7 26.8 + - - -
305H GLY 4.5 1.3 - - - -
306H SER* 1.3 83.1 - - - +
308H THR* 1.3 62.0 + - - +
309H PHE* 3.4 26.2 + - + -
391H ASP* 5.5 1.9 + - - -
396H ALA* 3.4 30.9 + - - +
406H GLN 4.0 0.2 - - - -
408H LEU* 3.9 18.6 - - + -
419H ARG 2.9 26.7 + - - -
420H ALA* 3.1 26.2 + - - +
422H ASN 4.7 3.4 + - - -
423H SER* 3.9 18.8 + - - -
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Residues in contact with THR 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ASN* 3.5 17.0 + - - +
277H ILE* 4.3 3.4 - - + -
290H ALA* 4.1 13.9 + - + +
305H GLY 3.7 12.6 + - - -
307H ARG* 1.3 71.0 + - - +
309H PHE* 1.3 54.3 + - - +
310H VAL* 3.7 5.2 + - + -
318H PHE* 4.0 32.8 - - + -
405H MET* 3.6 19.5 - - + +
406H GLN 2.9 18.7 + - - -
407H ILE* 3.4 7.2 - - - +
408H LEU* 2.8 32.6 + - - +
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Residues in contact with PHE 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H PRO* 4.0 18.2 - - + -
275H ASN 3.1 6.4 + - - +
276H ILE* 4.2 9.2 - - + -
277H ILE* 2.7 34.8 + - - +
307H ARG* 3.7 45.1 - - + -
308H THR* 1.3 72.0 - - - +
310H VAL* 1.3 55.3 + - - +
391H ASP* 4.1 2.7 - - - -
408H LEU* 3.4 37.9 - - + -
410H PHE* 3.7 19.4 - + + -
416H VAL* 3.7 22.0 - - + -
419H ARG* 3.7 41.3 - - + -
420H ALA* 4.3 4.5 - - - -
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Residues in contact with VAL 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE* 3.7 7.9 - - + -
308H THR* 3.9 7.9 - - + +
309H PHE* 1.3 77.4 - - - +
311H GLN* 1.3 70.1 + - - +
314H ILE* 4.0 12.3 - - + -
315H TYR* 3.8 22.7 - - + -
318H PHE* 3.5 57.7 - - + -
407H ILE* 3.7 15.3 - - + -
408H LEU 2.8 9.5 + - - +
409H LYS* 3.5 9.0 - - - +
410H PHE* 3.3 20.2 + - - -
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Residues in contact with GLN 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE 3.0 15.2 + - - +
278H MET* 5.1 3.8 - - + -
279H SER* 3.6 29.2 - - - +
310H VAL* 1.3 71.9 - - - +
312H GLU* 1.3 88.7 + - - +
313H ASP* 3.1 37.3 + - - +
314H ILE* 3.0 16.7 + - - +
315H TYR 3.1 8.8 + - - -
410H PHE* 3.2 28.1 - - + -
411H LYS* 2.6 36.9 + - - +
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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
------------------------------------------------------------
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