Contacts of the strand formed by residues 311 - 316 (chain B) in PDB entry 3I8E
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 ALA 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B VAL* 3.4 25.6 - - - +
260B CYS* 3.7 19.3 - - - -
274B GLY* 4.9 7.4 - - - -
275B ASP 4.8 4.2 + - - +
278B GLY 5.4 1.0 + - - +
308B THR* 4.7 2.5 - - - +
309B SER 2.7 7.0 + - - +
310B ILE* 1.3 73.2 - - - +
312B GLU* 1.3 62.0 + - - +
313B CYS 3.8 7.9 - - - +
314B LEU* 4.2 6.3 - - + -
324B VAL* 3.6 25.8 - - + -
325B GLY 3.4 5.6 - - - -
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL 4.1 12.9 - - - +
16B ASN* 4.7 12.1 - - - +
259B VAL* 4.9 14.1 - - - +
260B CYS* 3.0 27.8 - - - +
310B ILE* 3.4 4.1 + - + +
311B ALA* 1.3 72.6 - - - +
313B CYS* 1.3 59.6 + - - +
325B GLY 2.6 11.4 + - - +
327B ARG* 2.8 61.3 + - + +
328B LEU* 5.5 0.9 - - + +
165D SER* 5.5 0.9 + - - -
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Residues in contact with CYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.0 13.0 - - + -
16B ASN 5.1 1.3 - - - +
17B GLY* 3.9 10.5 - - - +
18B CYS* 2.1 71.8 - - - +
311B ALA* 3.8 4.0 - - - +
312B GLU* 1.3 81.1 - - - +
314B LEU* 1.3 70.4 + - - +
315B THR* 4.0 2.0 - - - -
324B VAL 3.7 1.2 - - - -
325B GLY* 2.8 29.7 + - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS 5.4 0.2 - - - +
260B CYS* 3.7 24.8 - - - +
261B HIS 4.2 9.6 + - - +
262B ASN* 3.4 19.0 - - + +
272B LEU* 3.6 42.8 - - + +
273B LEU 4.2 1.3 - - - +
274B GLY* 4.3 3.1 - - - +
280B LEU* 3.8 18.6 - - + -
308B THR* 5.7 0.2 - - - +
311B ALA* 4.2 5.6 - - + -
312B GLU 4.1 0.8 + - - -
313B CYS* 1.3 78.5 - - - +
315B THR* 1.3 69.9 + - - +
322B VAL* 3.9 21.8 - - + -
323B PHE 3.5 4.9 - - - +
324B VAL* 4.0 26.2 - - + -
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Residues in contact with THR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B CYS* 3.3 30.1 + - - -
19B VAL* 4.2 2.1 + - - -
20B THR* 3.6 29.8 - - + +
31B LEU* 3.9 17.7 - - + -
262B ASN* 3.4 8.6 + - - +
272B LEU* 4.9 0.2 - - - -
313B CYS* 4.0 1.2 - - - -
314B LEU* 1.3 84.7 + - - +
316B TYR* 1.3 74.7 + - - +
317B LEU* 3.7 3.9 + - + +
322B VAL* 3.6 3.5 - - - -
323B PHE* 2.8 38.0 + - - +
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Residues in contact with TYR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.1 10.6 + - - +
262B ASN* 3.2 9.4 + - - +
263B ARG 4.2 15.0 - - - +
264B VAL* 3.5 46.2 - - + -
270B ARG* 5.6 2.5 + - - -
272B LEU* 4.1 14.8 - - + +
315B THR* 1.3 83.0 - - - +
317B LEU* 1.3 78.2 + - - +
318B ASP 2.9 13.4 + - - -
319B ASN* 3.4 2.1 + - - -
320B GLY* 2.7 39.1 + - - -
321B VAL 3.2 17.0 - - - -
322B VAL* 3.7 15.0 - - + +
336B LEU* 5.0 5.6 - - + -
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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