Contacts of the helix formed by residues 300 - 310 (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 THR 300 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60I THR* 4.3 1.8 - - - -
64I GLN* 5.2 1.8 - - - +
297I LYS 5.1 3.1 - - - +
298I GLU* 3.1 15.5 + - - +
299I LEU* 1.3 76.3 - - - +
301I PRO* 1.3 73.4 - - - +
302I GLU* 3.3 18.6 + - - +
303I VAL* 2.9 31.0 + - + +
304I LEU* 2.8 22.3 + - - +
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Residues in contact with PRO 301 (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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53I LYS 5.5 0.2 - - - +
56I SER* 4.7 5.6 - - - +
57I ARG* 3.8 41.1 - - + +
60I THR* 3.7 33.8 - - + +
61I THR* 5.4 1.8 - - - +
300I THR* 1.3 82.0 - - - +
302I GLU* 1.3 72.0 + - - +
304I LEU* 3.9 5.6 - - + +
305I GLN* 2.8 31.1 + - - +
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Residues in contact with GLU 302 (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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57I ARG* 5.4 5.2 + - - +
300I THR* 3.3 15.4 - - - +
301I PRO* 1.3 96.8 - - - +
303I VAL* 1.3 63.8 + - + +
305I GLN* 3.9 6.5 - - - +
306I GLU* 3.1 24.9 + - - +
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Residues in contact with VAL 303 (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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298I GLU 4.3 13.2 - - - +
299I LEU* 4.5 7.4 - - + -
300I THR* 2.9 27.1 + - + +
302I GLU* 1.3 77.1 - - + +
304I LEU* 1.3 63.5 + - - +
306I GLU* 3.2 5.2 + - - +
307I TRP* 2.9 64.7 + - + +
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Residues in contact with LEU 304 (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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56I SER* 6.2 0.4 - - - -
60I THR* 4.6 7.0 - - - +
282I VAL* 5.9 0.7 - - + -
284I ILE* 4.0 27.4 - - + -
299I LEU* 3.8 22.0 - - + +
300I THR 2.8 14.3 + - - +
301I PRO* 3.9 4.7 - - + +
303I VAL* 1.3 79.8 - - - +
305I GLN* 1.3 63.4 + - - +
307I TRP* 3.3 7.2 + - + +
308I LEU* 3.3 42.4 + - + +
411I PHE* 3.9 32.8 - - + -
420I ILE* 4.1 20.9 - - + -
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Residues in contact with GLN 305 (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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39I LYS* 6.0 3.8 - - + -
49I TRP* 5.2 6.5 + - + +
53I LYS* 4.7 17.9 - - - +
56I SER* 5.8 2.6 + - - -
301I PRO 2.8 20.8 + - - +
302I GLU* 4.0 7.6 - - - +
304I LEU* 1.3 79.5 - - - +
306I GLU* 1.3 63.9 + - - +
308I LEU* 3.7 12.1 + - - +
309I ASP* 3.4 29.7 + - - +
413I ARG* 5.5 0.6 - - - +
418I ASN* 3.1 39.5 + - - +
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Residues in contact with GLU 306 (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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302I GLU 3.1 17.8 + - - +
303I VAL* 3.5 5.7 - - - +
304I LEU 3.2 0.2 - - - -
305I GLN* 1.3 79.5 - - - +
307I TRP* 1.3 74.4 + - - +
309I ASP* 3.0 22.0 + - + +
310I GLU* 2.4 47.0 - - - +
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Residues in contact with TRP 307 (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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261I ARG* 4.7 2.3 - - - +
263I VAL* 3.9 34.3 - - + +
264I ALA* 5.2 11.8 - - + +
267I THR* 4.2 15.5 - - + -
269I VAL* 4.0 19.5 - - + +
284I ILE* 3.3 43.1 - - + -
295I VAL* 4.5 12.3 - - + -
299I LEU* 3.7 20.4 - - + -
303I VAL* 2.9 41.5 + - + +
304I LEU* 3.3 9.6 + - + +
306I GLU* 1.3 86.4 - - - +
308I LEU* 1.3 63.7 + - + +
310I GLU* 3.1 27.8 + - - +
311I LEU* 4.0 8.6 + - - +
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Residues in contact with LEU 308 (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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259I ARG* 3.2 24.4 + - - -
269I VAL* 4.6 5.4 - - + -
282I VAL* 3.8 35.4 - - + -
304I LEU* 3.3 34.3 + - + +
305I GLN* 4.0 12.3 - - - +
307I TRP* 1.3 79.2 - - + +
309I ASP* 1.3 61.9 + - - +
310I GLU 3.3 0.5 + - - -
311I LEU* 3.4 22.9 + - + +
413I ARG* 3.4 46.9 - - - +
418I ASN* 5.5 0.9 - - - +
420I ILE* 6.3 0.7 - - + -
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Residues in contact with ASP 309 (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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39I LYS* 4.2 22.4 - - - +
259I ARG* 5.2 1.7 + - - -
305I GLN* 3.4 28.4 + - - +
306I GLU* 3.0 18.1 + - + +
308I LEU* 1.3 78.6 - - - +
310I GLU* 1.3 57.8 + - + +
311I LEU 3.5 2.4 + - - +
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Residues in contact with GLU 310 (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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261I ARG* 3.2 50.3 + - - +
262I ARG 4.8 0.2 - - - +
263I VAL* 3.6 10.9 - - - +
306I GLU* 2.4 42.4 - - - +
307I TRP* 3.1 20.8 - - - +
308I LEU 3.2 0.2 - - - -
309I ASP* 1.3 75.5 - - + +
311I LEU* 1.3 59.0 + - - +
312I GLU* 3.6 1.4 + - - +
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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