Contacts of the strand formed by residues 312 - 321 (chain I) in PDB entry 2B4X
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 GLU 312 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259I ARG* 3.9 2.9 - - - -
260I TYR* 2.9 29.4 + - - +
261I ARG* 3.6 20.9 - - - +
310I GLU 3.6 1.9 + - - +
311I LEU* 1.3 75.1 - - - +
313I GLU* 1.3 95.3 + - - +
314I MET* 3.4 9.7 + - + +
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Residues in contact with GLU 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I LYS* 2.9 51.8 + - + +
258I PHE* 4.6 4.3 - - - +
259I ARG* 4.0 19.6 - - + +
312I GLU* 1.3 91.4 + - - +
314I MET* 1.3 72.2 + - - +
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Residues in contact with MET 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I GLY 3.3 0.9 - - - +
257I LYS* 3.1 6.2 - - - -
258I PHE 2.8 40.5 + - - +
260I TYR* 4.7 7.0 - - + -
261I ARG* 4.2 27.1 - - - -
312I GLU* 4.0 11.4 - - + +
313I GLU* 1.3 88.3 - - - +
315I MET* 1.3 64.4 + - - +
316I LEU* 3.7 11.2 - - + +
400I VAL* 3.5 32.5 - - + -
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Residues in contact with MET 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I GLY* 3.5 12.3 - - - -
257I LYS* 4.2 6.5 - - - +
314I MET* 1.3 77.2 - - - +
316I LEU* 1.3 65.6 + - - +
395I LEU* 5.4 8.5 - - - -
399I ARG* 4.3 18.2 - - - +
400I VAL* 4.4 5.0 + - - +
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Residues in contact with LEU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I GLU* 3.3 7.5 - - - +
256I GLY 3.2 29.8 + - - +
258I PHE* 3.8 8.9 - - + +
260I TYR* 3.6 39.0 - - + -
270I LEU* 4.3 10.1 - - + -
314I MET* 3.7 23.1 - - + +
315I MET* 1.3 74.8 - - - +
317I VAL* 1.3 63.4 + - - +
318I VAL* 3.5 34.0 + - + +
395I LEU* 5.4 0.8 - - - +
399I ARG* 4.4 7.0 - - - +
400I VAL* 3.6 22.9 - - + +
402I PHE* 4.2 18.6 - - + +
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Residues in contact with VAL 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253I TYR* 3.3 34.5 - - + +
254I GLN 3.8 2.5 - - - -
255I GLU* 3.6 12.3 - - - +
316I LEU* 1.3 75.2 - - - +
318I VAL* 1.3 59.3 + - - +
319I HIS* 3.4 17.9 + - + -
399I ARG* 3.3 32.3 - - + +
400I VAL 3.3 10.8 + - - +
401I THR* 3.7 10.3 + - - +
402I PHE 2.9 27.4 + - - +
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Residues in contact with VAL 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229I PHE* 3.9 24.0 - - + -
252I MET 3.9 0.2 - - - +
253I TYR* 3.5 9.7 - - - -
254I GLN* 2.9 41.4 + - + +
258I PHE* 4.3 20.9 - - + -
270I LEU* 3.6 27.8 - - + -
272I LEU* 4.7 3.4 - - + -
316I LEU* 3.5 26.7 + - + +
317I VAL* 1.3 71.7 - - - +
319I HIS* 1.3 72.9 + - - +
320I MET* 4.2 5.6 - - + +
402I PHE* 3.5 4.0 - - + +
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Residues in contact with HIS 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I ARG* 6.4 0.2 - - - -
237I GLU* 4.2 13.4 + - - -
251I MET* 4.1 11.9 - - + -
252I MET 3.5 5.2 - - - -
253I TYR* 3.3 24.7 - + + -
317I VAL* 3.4 33.3 + - + +
318I VAL* 1.3 72.4 - - - +
320I MET* 1.3 61.4 + - - +
401I THR* 4.5 6.5 + - - -
402I PHE* 2.8 11.4 + - - +
403I LYS* 3.4 53.7 + - + +
404I ALA* 2.8 28.9 + - - +
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Residues in contact with MET 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I TRP* 4.6 2.2 - - - -
229I PHE* 3.9 13.0 - - + -
251I MET* 3.6 4.2 - - - -
252I MET* 3.0 48.1 + - + +
272I LEU* 3.5 30.3 - - - -
281I MET* 3.2 29.8 - - + -
283I LEU* 3.4 20.9 - - + -
318I VAL* 4.1 8.5 - - + +
319I HIS* 1.3 75.9 - - - +
321I PRO* 1.3 68.5 - - + +
323I PHE* 3.8 21.8 - - + -
375I VAL* 4.7 2.9 - - + -
402I PHE* 5.2 0.7 - - + -
404I ALA* 4.7 1.8 - - + -
408I PHE* 4.5 4.3 - - + -
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Residues in contact with PRO 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239I PHE* 4.5 1.3 - - + -
249I ALA* 4.6 6.3 - - + -
250I SER 3.5 10.3 - - - +
251I MET* 3.3 17.3 - - + -
252I MET* 4.1 2.4 - - - +
320I MET* 1.3 97.9 - - + +
322I ARG* 1.3 68.3 + - - +
323I PHE* 3.4 14.5 - - + -
375I VAL* 5.2 0.2 - - - +
404I ALA* 3.3 28.0 - - + +
408I PHE* 4.0 20.9 - - + -
429I PRO* 4.0 24.9 - - + -
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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
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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