Contacts of the strand formed by residues 306 - 311 (chain A) in PDB entry 3RAW
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 CYS 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLN* 4.3 13.9 - - - +
300A TYR* 3.6 9.1 - - - -
301A ASN* 2.8 34.8 + - - +
304A LYS* 3.2 13.9 - - + +
305A SER* 1.3 77.7 - - - +
307A GLU* 1.3 65.1 + - - +
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Residues in contact with GLU 307 (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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253A GLN* 3.1 20.0 + - - +
298A THR* 3.7 25.3 - - + +
299A LEU 3.3 8.5 - - - +
300A TYR* 3.8 17.9 - - + +
306A CYS* 1.3 79.9 - - - +
308A GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 308 (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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250A ASN* 4.0 9.2 - - - +
253A GLN* 3.4 32.8 - - - +
254A PRO* 4.7 9.8 - - - +
297A GLU 3.7 0.3 - - - +
298A THR* 3.3 3.8 - - - +
299A LEU* 2.8 49.1 + - + +
301A ASN* 2.8 38.6 + - + +
306A CYS 4.5 2.5 - - - +
307A GLU* 1.3 75.4 - - - +
309A LYS* 1.3 72.5 + - - +
310A SER* 5.6 0.4 - - - -
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Residues in contact with LYS 309 (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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246A PHE* 4.1 14.8 - - + +
249A GLU* 3.4 40.3 + - + +
250A ASN* 3.0 38.2 + - + +
256A PRO* 5.7 2.9 - - - +
296A PHE* 3.8 49.6 - - + -
297A GLU 3.4 4.3 - - - -
298A THR* 4.4 9.0 - - + +
308A GLU* 1.3 80.3 - - - +
310A SER* 1.3 60.5 + - - +
311A VAL 4.2 0.2 - - - -
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Residues in contact with SER 310 (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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256A PRO* 4.8 8.8 - - - +
259A HIS* 3.5 21.1 + - - -
296A PHE* 3.2 2.8 - - - +
297A GLU* 2.8 45.4 + - - +
299A LEU* 4.3 21.6 - - - +
309A LYS* 1.3 74.6 - - - +
311A VAL* 1.3 67.7 + - - +
312A LYS 3.4 0.2 + - - -
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Residues in contact with VAL 311 (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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246A PHE* 3.7 26.3 - - + -
255A TYR* 5.4 1.7 - - + -
259A HIS* 3.3 22.3 + - + +
291A PHE* 4.1 19.7 - - + -
293A ASN 3.9 1.1 - - - +
294A SER* 3.9 22.0 - - - -
295A GLU 3.5 16.4 - - - +
297A GLU* 5.9 0.2 - - - -
310A SER* 1.3 74.8 + - - +
312A LYS* 1.3 60.6 + - - +
313A ASN 3.7 20.9 - - - +
314A THR* 3.5 30.0 - - + +
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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