Contacts of the helix formed by residues 348 - 362 (chain I) in PDB entry 2I2X
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 ASN 348 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343I ALA* 2.9 7.7 + - - +
346I THR* 3.0 33.5 + - - +
347I LYS* 1.3 79.5 + - - +
349I ASP* 1.3 63.6 + - - +
350I LYS 3.5 2.0 - - - -
351I VAL* 3.2 28.8 - - + +
352I LEU* 3.3 10.0 + - - +
351K VAL* 3.6 22.9 - - - +
355K LEU* 4.0 17.4 - - + +
2L LEU* 3.5 18.7 - - - +
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Residues in contact with ASP 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I THR* 2.7 33.4 + - - +
19I PHE* 3.7 26.0 - - + -
343I ALA* 3.5 10.5 + - - +
344I LEU* 3.9 24.8 - - + +
347I LYS* 3.5 17.3 - - - +
348I ASN* 1.3 78.6 + - - +
350I LYS* 1.3 68.4 + - - +
352I LEU* 3.1 3.5 + - - +
353I ARG* 2.8 29.3 + - - +
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Residues in contact with LYS 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP* 3.4 34.1 + - - +
16I GLU* 4.6 14.6 + - - +
17I MET 4.9 1.1 - - - -
18I THR* 4.8 6.1 - - - +
347I LYS 5.5 0.2 + - - -
348I ASN 3.5 0.6 - - - -
349I ASP* 1.3 91.6 + - - +
351I VAL* 1.3 57.3 + - - +
353I ARG* 3.3 32.3 + - - +
354I ASP* 2.9 34.3 + - - -
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Residues in contact with VAL 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I ASN* 3.2 34.5 - - + +
350I LYS* 1.3 73.7 - - - +
352I LEU* 1.3 61.4 + - + +
354I ASP* 3.4 6.6 + - - +
355I LEU* 2.9 33.3 + - + +
2J LEU* 4.4 10.8 - - + -
348K ASN* 3.8 33.9 - - + +
351K VAL* 4.5 14.8 - - + -
355K LEU* 5.6 1.8 - - + -
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Residues in contact with LEU 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 4.0 11.2 - - + -
339I LEU* 4.1 28.5 - - + +
340I MET* 4.2 10.1 - - + -
343I ALA* 3.7 22.7 - - + -
348I ASN 3.3 12.9 + - - +
349I ASP 3.1 8.5 + - - +
351I VAL* 1.3 77.1 - - - +
353I ARG* 1.3 64.0 + - - +
355I LEU* 3.1 16.9 + - + +
356I MET* 2.9 49.5 + - + +
339K LEU* 4.6 6.7 - - + -
352K LEU* 4.4 20.4 - - + -
355K LEU* 4.4 11.2 - - + -
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Residues in contact with ARG 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP* 2.6 49.5 + - - +
17I MET 3.1 23.2 + - - +
18I THR* 4.6 3.3 - - - +
19I PHE* 3.9 4.6 - - + -
305I GLN* 3.5 29.1 - - + +
306I CYS* 4.6 1.3 - - - -
349I ASP 2.8 17.3 + - - +
350I LYS* 3.4 32.6 + - - +
352I LEU* 1.3 75.9 - - - +
354I ASP* 1.3 96.4 + - - +
356I MET* 3.3 14.7 + - - +
357I MET* 3.0 24.4 + - - +
372I TYR* 3.1 33.3 + - + -
1J MET* 5.3 0.6 - - - +
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Residues in contact with ASP 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350I LYS* 2.9 19.6 + - - +
351I VAL* 3.7 4.5 - - - +
353I ARG* 1.3 93.3 + - - +
355I LEU* 1.3 56.1 + - - +
357I MET* 3.8 9.5 - - + +
358I LEU* 2.9 32.4 + - - +
372I TYR* 2.5 29.3 + - - -
1J MET* 2.9 31.3 + - - -
2J LEU* 3.7 27.8 + - + +
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Residues in contact with LEU 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351I VAL* 2.9 22.5 + - + +
352I LEU* 3.1 17.0 + - + +
354I ASP* 1.3 75.6 - - - +
356I MET* 1.3 63.1 + - - +
358I LEU 3.3 0.5 + - - -
359I SER* 3.0 22.5 + - - -
2J LEU* 3.5 18.8 - - + -
339K LEU* 3.9 14.1 - - + +
342K THR* 3.6 16.0 - - + +
343K ALA* 3.8 34.1 - - + +
346K THR* 3.5 24.5 - - - +
348K ASN* 4.1 13.7 - - + +
351K VAL* 5.6 1.8 - - + -
352K LEU* 4.5 16.6 - - + -
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Residues in contact with MET 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 3.5 19.3 - - + -
301I ASN* 3.4 15.9 - - - +
302I LEU* 3.2 20.9 + - - +
304I MET* 3.3 32.5 - - + +
305I GLN* 3.1 36.8 - - - +
339I LEU* 6.5 0.4 - - - -
340I MET* 4.6 5.8 - - - -
352I LEU* 2.9 30.4 + - + +
353I ARG* 3.6 10.5 - - - -
355I LEU* 1.3 74.7 - - - +
357I MET* 1.3 63.2 + - - +
359I SER* 3.3 13.0 - - - -
339K LEU* 3.7 24.0 - - + -
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Residues in contact with MET 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I LEU* 3.4 16.5 - - - +
305I GLN* 3.3 25.3 - - + +
353I ARG 3.0 17.3 + - - +
354I ASP* 3.9 16.2 - - + +
356I MET* 1.3 76.5 - - - +
358I LEU* 1.3 64.6 + - + +
360I ASP 3.3 2.8 + - - -
361I ARG* 3.0 54.5 + - - +
371I ALA* 3.6 16.2 - - + -
372I TYR* 3.9 17.5 - - + -
1J MET* 3.7 30.1 - - - -
2J LEU 4.1 12.1 - - - +
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Residues in contact with LEU 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354I ASP 2.9 17.0 + - - +
357I MET* 1.3 81.1 - - + +
359I SER* 1.3 66.5 + - - +
360I ASP 2.9 3.9 + - - -
361I ARG* 3.6 11.2 + - + +
362I TYR* 3.9 21.6 + - + -
2J LEU* 3.8 15.0 - - + +
3J ASP* 3.6 39.0 - - - +
4J PHE* 3.4 45.2 - - + +
13J LEU* 5.5 0.3 - - - +
342K THR* 3.8 9.4 - - + -
346K THR* 3.9 15.3 - - + -
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Residues in contact with SER 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I ASN* 3.0 28.5 + - - +
355I LEU 3.0 12.9 + - - -
356I MET* 3.3 16.2 - - - -
358I LEU* 1.3 77.0 - - - +
360I ASP* 1.3 70.0 + - - +
363I ARG* 3.2 14.6 + - - -
4J PHE* 5.1 0.2 - - - -
12J VAL* 4.2 4.7 - - - +
13J LEU* 3.7 10.2 - - - +
338K ALA* 3.6 16.8 - - - +
339K LEU* 4.7 2.2 - - - -
342K THR* 3.4 18.8 + - - -
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Residues in contact with ASP 360 (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 VAL 4.0 10.8 - - - +
299I MET* 3.3 8.1 - - - -
301I ASN* 2.8 31.7 + - - -
302I LEU* 2.9 25.2 + - + -
357I MET 3.3 1.8 + - - -
358I LEU 3.0 0.2 - - - -
359I SER* 1.3 92.6 + - - +
361I ARG* 1.3 66.2 + - - +
362I TYR 2.8 6.4 + - - -
363I ARG* 2.8 42.5 + - - +
367I ALA* 3.2 13.8 - - + +
335K TYR* 3.3 11.7 - - - -
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Residues in contact with ARG 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302I LEU* 4.1 8.5 - - + -
357I MET* 3.0 40.7 + - - +
358I LEU* 3.6 9.6 + - - -
360I ASP* 1.3 75.4 - - - +
362I TYR* 1.3 93.1 + - + +
364I ASP 4.2 0.5 - - - +
368I TYR* 3.1 57.8 + - + +
371I ALA* 3.5 10.4 - - + +
373I ASP* 2.2 48.2 + - - -
374I ASN* 3.6 18.8 + - - +
1J MET* 4.2 4.8 - - - -
2J LEU 5.8 0.8 + - - -
3J ASP* 4.5 4.3 - - - -
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Residues in contact with TYR 362 (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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358I LEU* 3.9 12.2 + - + -
360I ASP 2.8 2.8 + - - -
361I ARG* 1.3 96.0 + - + +
363I ARG* 1.3 63.7 + - - +
364I ASP 3.3 2.2 - - - -
368I TYR* 3.8 23.5 + + - -
407I GLY 5.4 0.2 - - - -
411I LYS* 3.5 33.4 + - + +
412I LEU* 3.8 31.0 - - + +
413I GLU 5.4 0.7 + - - -
3J ASP* 2.6 36.4 + - - -
4J PHE* 4.1 12.8 - + - -
9J LEU* 3.7 37.5 - - + -
13J LEU* 3.8 15.3 - - + +
15J ARG* 3.8 11.3 - - - +
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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
------------------------------------------------------------
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