Contacts of the helix formed by residues 298 - 309 (chain A) in PDB entry 2I91
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 SER 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ALA* 2.5 34.2 + - - -
296A PRO 3.0 5.0 + - - -
297A ALA* 1.3 85.3 - - - +
299A SER* 1.3 63.8 + - - +
300A GLU* 3.8 17.5 + - - +
301A VAL* 3.1 23.8 + - - +
302A SER* 3.3 19.6 + - - -
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Residues in contact with SER 299 (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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298A SER* 1.3 71.8 - - - +
300A GLU* 1.3 64.7 + - - +
302A SER* 2.9 11.4 + - - -
303A SER* 2.8 34.4 + - - -
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Residues in contact with GLU 300 (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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270A LYS* 3.1 39.0 + - + -
273A LEU* 3.8 18.5 - - + +
293A VAL 3.1 25.4 - - - +
294A LEU* 3.7 8.5 - - + -
298A SER* 3.9 12.6 - - - +
299A SER* 1.3 86.4 + - - +
301A VAL* 1.3 58.7 + - - +
303A SER* 3.1 10.7 + - - -
304A VAL* 2.9 30.5 + - - +
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Residues in contact with VAL 301 (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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294A LEU* 3.4 43.1 - - + +
295A ALA 3.4 6.1 - - - +
296A PRO* 5.1 0.2 - - + -
297A ALA 5.2 3.4 - - - +
298A SER* 3.1 24.7 + - - +
300A GLU* 1.3 79.4 - - - +
302A SER* 1.3 66.7 + - - +
304A VAL* 3.1 13.3 + - - +
305A CYS* 3.1 13.2 + - - -
346A ASP* 3.7 21.8 - - - +
348A SER* 4.2 11.2 - - - +
349A ILE* 3.6 21.5 - - + -
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Residues in contact with SER 302 (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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298A SER 3.3 10.6 + - - -
299A SER* 2.9 16.5 + - - -
301A VAL* 1.3 82.1 - - - +
303A SER* 1.3 60.7 + - - +
305A CYS* 3.5 6.5 + - - +
306A GLU* 3.2 33.6 + - - +
348A SER* 6.2 0.2 - - - -
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Residues in contact with SER 303 (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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273A LEU* 5.7 3.6 - - - -
274A GLN 5.6 2.3 + - - -
299A SER 2.8 11.3 + - - -
300A GLU* 3.2 14.4 - - - -
302A SER* 1.3 76.4 - - - +
304A VAL* 1.3 63.1 + - - +
306A GLU* 3.1 16.9 + - - +
307A ARG* 3.1 28.3 + - - +
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Residues in contact with VAL 304 (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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273A LEU* 3.9 13.0 - - + -
281A LEU* 3.8 28.7 - - + +
285A LEU* 3.8 17.0 - - + -
294A LEU* 3.7 21.1 - - + -
300A GLU 2.9 16.5 + - - +
301A VAL 3.4 7.9 - - - +
303A SER* 1.3 74.3 - - - +
305A CYS* 1.3 65.0 + - - +
307A ARG* 2.9 16.4 + - - +
308A LEU* 2.9 36.9 + - + +
349A ILE* 3.8 12.3 - - + -
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Residues in contact with CYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A VAL* 3.1 11.6 + - - -
302A SER* 3.8 9.0 - - - +
304A VAL* 1.3 80.0 - - - +
306A GLU* 1.3 60.2 + - - +
308A LEU* 3.5 1.0 + - - +
309A THR* 2.9 32.7 + - - +
348A SER* 3.5 36.1 - - - -
349A ILE* 3.4 27.6 - - - -
351A GLU* 6.2 0.2 - - - +
352A ALA* 3.8 17.0 - - + -
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Residues in contact with GLU 306 (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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302A SER* 3.2 20.5 + - - +
303A SER* 3.1 12.8 + - - +
305A CYS* 1.3 79.4 - - - +
307A ARG* 1.3 63.1 + - + +
309A THR* 3.7 11.6 + - - +
310A ASN* 3.8 15.1 + - - +
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Residues in contact with ARG 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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273A LEU* 3.9 11.1 + - - +
274A GLN 4.5 5.5 + - - -
275A ASP* 4.1 7.4 + - - +
276A MET* 2.7 43.0 + - - +
278A LEU* 3.7 42.8 - - + +
281A LEU* 4.0 17.2 - - + +
303A SER* 3.4 24.9 - - - +
304A VAL* 2.9 7.4 + - - +
306A GLU* 1.3 77.2 - - + +
308A LEU* 1.3 66.2 + - - +
309A THR 3.1 3.6 + - - -
310A ASN* 3.1 22.7 + - - +
313A LEU* 4.9 15.3 - - + +
314A LEU* 4.6 0.2 - - - +
14D A 5.8 0.4 + - - -
15D A 4.1 7.5 + - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LEU* 4.8 9.0 - - + +
281A LEU* 4.5 17.9 - - + -
282A LEU* 3.8 27.8 - - + -
285A LEU* 4.2 8.7 - - + -
304A VAL* 2.9 41.0 + - + +
305A CYS* 4.0 3.8 - - - +
307A ARG* 1.3 76.5 - - - +
309A THR* 1.3 59.0 + - + +
310A ASN 3.4 0.7 - - - -
314A LEU* 3.1 23.0 - - + +
324A ILE* 5.8 0.9 - - + -
349A ILE* 4.5 4.7 - - + -
352A ALA* 4.6 12.1 - - + +
353A LEU* 3.8 22.7 - - + -
356A ALA* 3.0 30.0 - - + +
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Residues in contact with THR 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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305A CYS* 2.9 19.8 + - + +
306A GLU* 3.7 8.3 + - - -
307A ARG 3.1 0.4 - - - -
308A LEU* 1.3 76.0 - - - +
310A ASN* 1.3 58.9 + - - +
311A GLU 3.4 1.7 + - - -
314A LEU* 4.5 0.4 - - - -
352A ALA* 3.3 37.2 - - + +
355A ASN* 4.1 13.0 - - + -
356A ALA* 4.4 1.8 - - - +
359A LYS* 3.3 40.7 + - - +
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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