Contacts of the helix formed by residues 300 - 314 (chain A) in PDB entry 3IND
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 LYS 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A TYR* 6.1 1.8 - - + -
298A LEU 3.5 0.2 + - - -
299A PRO* 1.3 71.9 - - - +
301A LYS* 1.3 63.8 + - - +
303A PHE* 3.2 1.2 + - - +
304A GLU* 3.1 51.1 + - - +
388A GLN* 3.1 35.6 + - + +
389A SER 3.3 9.6 + - - +
390A SER* 4.4 14.6 + - - +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A MET* 3.4 29.6 - - + +
281A GLU* 3.9 27.6 - - - +
284A TYR* 6.4 0.9 - - + -
299A PRO* 3.2 2.7 - - + +
300A LYS* 1.3 79.6 - - - +
302A VAL* 1.3 61.2 + - + +
304A GLU* 3.8 10.8 + - - +
305A ALA* 3.4 22.2 + - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 5.1 5.2 - - + -
275A LEU* 4.2 14.8 - - + +
277A MET* 3.7 24.0 - - + -
281A GLU* 3.4 26.7 - - + +
282A TYR* 3.8 25.8 - - + -
298A LEU* 4.3 21.5 - - + -
299A PRO* 2.9 16.8 + - + +
301A LYS* 1.3 75.4 - - + +
303A PHE* 1.3 61.2 + - - +
305A ALA* 3.3 2.5 + - - +
306A ALA* 2.9 28.7 + - + +
393A THR* 5.8 0.2 - - - +
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.8 20.5 - - + +
299A PRO 2.8 19.6 + - - +
300A LYS 3.6 3.1 - - - +
302A VAL* 1.3 73.8 - - - +
304A GLU* 1.3 63.7 + - + +
306A ALA* 3.1 3.3 + - - +
307A VAL* 2.8 56.4 + - + +
324A TRP 3.9 16.4 - - - -
325A LEU* 5.3 14.4 - - + -
386A ILE* 3.4 35.0 - - + -
387A SER* 3.4 24.2 - - - -
388A GLN* 3.6 31.9 - - + -
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Residues in contact with GLU 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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300A LYS* 3.1 42.8 + - - +
301A LYS* 4.1 8.6 - - - +
303A PHE* 1.3 86.7 - - + +
305A ALA* 1.3 59.2 + - - +
307A VAL* 3.4 4.5 + - - +
308A LYS* 2.9 31.6 + - - +
388A GLN* 4.5 4.9 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.8 26.1 - - + +
277A MET* 4.3 11.0 - - + -
301A LYS 3.4 15.6 + - - +
302A VAL 3.3 4.4 + - - +
303A PHE 3.3 0.6 - - - -
304A GLU* 1.3 78.0 - - - +
306A ALA* 1.3 61.4 + - - +
308A LYS* 3.8 9.5 + - - +
309A SER* 3.3 22.0 + - - -
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 6.2 0.7 - - + -
270A ILE* 4.5 20.6 - - + +
275A LEU* 4.5 6.0 - - + +
298A LEU* 4.0 21.3 - - + -
302A VAL* 2.9 18.1 + - + +
303A PHE 3.4 4.3 - - - +
305A ALA* 1.3 74.5 - - - +
307A VAL* 1.3 60.5 + - + +
309A SER* 3.1 4.6 + - - -
310A ILE* 2.9 40.8 + - + +
345A ILE* 6.1 0.7 - - + -
386A ILE* 5.5 2.7 - - + -
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Residues in contact with VAL 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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303A PHE* 2.8 58.5 + - + +
304A GLU* 3.9 4.0 - - - +
306A ALA* 1.3 69.4 - - + +
308A LYS* 1.3 56.8 + - - +
310A ILE* 3.1 7.8 + - + +
311A LYS* 2.7 66.4 + - + +
324A TRP* 4.3 14.4 - - + +
384A PHE* 4.0 17.5 - - + -
386A ILE* 5.5 0.9 - - + -
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Residues in contact with LYS 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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304A GLU 2.9 18.8 + - - +
305A ALA* 3.8 8.7 - - - +
307A VAL* 1.3 76.9 - - - +
309A SER* 1.3 63.7 + - - +
311A LYS* 3.3 10.2 + - - +
312A ALA* 3.0 24.1 + - + +
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Residues in contact with SER 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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270A ILE* 3.1 38.2 + - - +
273A GLN* 5.2 7.4 - - - +
275A LEU* 4.7 5.5 - - - +
305A ALA 3.3 10.9 + - - -
306A ALA 3.1 8.8 + - - -
308A LYS* 1.3 80.9 - - - +
310A ILE* 1.3 57.8 + - - +
312A ALA* 3.5 6.8 + - - +
313A ALA* 3.1 27.5 + - - +
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Residues in contact with ILE 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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270A ILE* 4.0 17.3 - - + -
306A ALA* 2.9 30.5 + - + +
307A VAL* 3.7 3.6 - - - +
309A SER* 1.3 74.6 - - - +
311A LYS* 1.3 64.6 + - - +
313A ALA* 3.4 1.6 + - - +
314A SER* 2.9 26.5 + - - -
324A TRP* 3.6 23.8 - - + -
342A PHE* 4.5 6.7 - - + -
343A PRO* 4.0 22.9 - - + -
345A ILE* 4.1 23.3 - - + -
367A TYR* 4.2 11.9 - - + +
384A PHE* 3.9 23.1 - - + -
386A ILE* 4.1 4.9 - - + -
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 2.7 46.8 + - + +
308A LYS* 3.6 8.5 - - - +
310A ILE* 1.3 73.0 - - - +
312A ALA* 1.3 62.3 + - - +
314A SER* 3.5 2.8 + - - -
315A SER* 3.1 21.1 + - - -
318A LYS* 4.1 7.0 + - - +
321A ASP* 5.1 8.7 - - - +
324A TRP* 3.5 51.9 - - + +
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Residues in contact with ALA 312 (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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308A LYS* 3.0 17.7 + - + +
309A SER* 3.7 7.2 - - - +
310A ILE 3.2 0.2 - - - -
311A LYS* 1.3 74.9 - - - +
313A ALA* 1.3 66.3 + - - +
315A SER* 2.9 26.6 + - - -
318A LYS* 5.5 0.9 - - - +
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Residues in contact with ALA 313 (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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271A ASN* 4.1 12.1 - - + +
309A SER 3.1 15.3 + - - +
310A ILE 3.9 0.2 - - - +
312A ALA* 1.3 79.4 - - - +
314A SER* 1.3 55.8 - - - +
315A SER* 3.7 2.4 + - - -
316A THR* 5.2 2.1 + - - +
341A ILE* 3.0 14.9 - - - +
343A PRO* 3.6 35.4 - - + -
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Residues in contact with SER 314 (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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310A ILE 2.9 19.3 + - - -
311A LYS 3.5 4.8 + - - -
312A ALA 3.1 0.8 - - - -
313A ALA* 1.3 74.8 - - - +
315A SER* 1.3 64.7 + - - +
316A THR 3.1 6.4 + - - +
317A GLU 3.4 14.2 - - - +
318A LYS* 4.8 2.1 - - - +
319A PHE* 4.1 5.6 - - - -
324A TRP* 3.8 19.4 - - - -
341A ILE* 3.3 29.6 - - - +
342A PHE* 4.0 20.6 - - - -
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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