Contacts of the helix formed by residues 348 - 361 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351I VAL* 3.8 21.3 - - - +
355I LEU* 4.1 14.3 - - + +
2J LEU* 3.7 21.0 - - - +
343K ALA* 2.7 16.8 + - - +
346K THR* 3.2 26.3 + - - +
347K LYS* 1.3 79.0 + - - +
349K ASP* 1.3 67.0 + - - +
350K LYS 3.4 2.5 - - - -
351K VAL* 3.3 29.1 - - + +
352K LEU* 3.4 6.9 + - - +
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Residues in contact with ASP 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K THR* 2.7 38.7 + - - +
19K PHE* 3.7 26.9 - - + -
343K ALA* 3.4 5.5 + - - -
344K LEU* 3.9 25.9 - - + +
347K LYS* 4.0 9.0 - - - -
348K ASN* 1.3 84.3 + - - +
350K LYS* 1.3 65.0 + - - +
352K LEU* 3.0 3.6 + - - +
353K ARG* 2.7 35.7 + - - +
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Residues in contact with LYS 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 4.4 12.5 + - - -
15K ASP* 2.8 40.8 + - - +
16K GLU* 4.1 13.5 + - - +
17K MET 4.7 1.8 - - - -
18K THR* 4.6 4.5 - - - +
348K ASN 3.4 1.2 - - - -
349K ASP* 1.3 90.2 + - - +
351K VAL* 1.3 57.6 + - - +
353K ARG* 3.4 29.4 + - - +
354K ASP* 3.0 33.8 + - - +
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Residues in contact with VAL 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I ASN* 3.6 36.6 - - + +
351I VAL* 4.5 14.8 - - + -
355I LEU* 5.6 2.5 - - + -
348K ASN* 3.3 31.1 + - + +
350K LYS* 1.3 77.0 - - - +
352K LEU* 1.3 61.2 + - + +
354K ASP* 3.2 7.4 + - - +
355K LEU* 2.9 33.1 + - + +
2L LEU* 4.3 10.3 - - + -
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Residues in contact with LEU 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339I LEU* 4.3 23.3 - - + -
352I LEU* 4.4 13.5 - - + -
355I LEU* 4.5 12.1 - - + -
19K PHE* 4.1 11.2 - - + -
339K LEU* 4.2 26.0 - - + +
340K MET* 4.3 7.9 - - + -
343K ALA* 3.8 22.0 - - + -
348K ASN 3.4 7.2 + - - +
349K ASP 3.0 8.5 + - - +
351K VAL* 1.3 78.7 - - - +
353K ARG* 1.3 65.4 + - - +
355K LEU* 3.2 10.7 + - + -
356K MET* 2.9 46.2 + - + +
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Residues in contact with ARG 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ALA 4.3 0.2 + - - -
15K ASP* 2.6 50.3 + - - +
17K MET 3.0 23.8 + - - +
18K THR* 4.4 3.3 - - - +
19K PHE* 3.8 3.8 - - + -
305K GLN* 3.3 29.4 - - + +
306K CYS* 4.7 1.1 - - - -
349K ASP 2.7 20.4 + - - +
350K LYS* 3.5 31.1 + - - +
352K LEU* 1.3 72.5 - - - +
354K ASP* 1.3 90.1 + - - +
356K MET* 2.8 15.6 + - + +
357K MET* 3.1 22.3 + - - +
372K TYR* 2.9 40.4 + - + -
1L MET* 5.3 0.2 - - - +
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Residues in contact with ASP 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350K LYS 3.0 19.2 + - - +
351K VAL* 3.2 5.0 + - - +
353K ARG* 1.3 93.2 + - - +
355K LEU* 1.3 57.8 + - - +
357K MET* 3.5 8.9 + - + +
358K LEU* 2.9 32.6 + - - +
372K TYR* 2.6 28.9 + - - -
1L MET* 3.0 23.9 + - - -
2L LEU* 3.3 32.1 + - + +
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Residues in contact with LEU 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339I LEU* 3.9 13.9 - - + +
342I THR* 3.6 13.7 - - + +
343I ALA* 4.2 28.9 - - + +
346I THR* 3.7 14.4 - - - +
348I ASN* 4.0 17.7 - - + +
351I VAL* 5.6 1.6 - - + -
352I LEU* 4.4 18.2 - - + -
351K VAL* 2.9 19.0 + - + +
352K LEU* 3.2 17.7 + - + +
354K ASP* 1.3 73.6 - - - +
356K MET* 1.3 65.1 + - - +
358K LEU* 3.3 0.4 + - - -
359K SER* 3.1 25.1 + - - -
2L LEU* 3.1 35.2 - - + -
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Residues in contact with MET 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339I LEU* 3.8 20.2 - - + +
19K PHE* 3.5 16.6 - - + -
301K ASN* 3.5 14.4 - - - +
302K LEU* 3.3 19.3 + - - +
304K MET* 3.6 38.1 - - + -
305K GLN* 3.6 15.9 - - - +
340K MET* 4.6 6.5 - - - -
352K LEU* 2.9 28.4 + - + +
353K ARG* 2.8 42.2 - - - +
355K LEU* 1.3 76.6 - - - +
357K MET* 1.3 62.2 + - - +
359K SER* 3.3 12.8 - - - -
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Residues in contact with MET 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K LEU* 3.2 18.8 - - + +
305K GLN* 3.5 23.5 - - + +
353K ARG 3.1 15.8 + - - +
354K ASP* 3.7 21.5 - - + +
356K MET* 1.3 75.7 - - - +
358K LEU* 1.3 65.0 + - + +
360K ASP 3.2 3.6 + - - -
361K ARG* 2.9 55.1 + - - +
371K ALA* 3.7 15.3 - - + -
372K TYR* 4.1 13.7 - - + -
1L MET* 3.6 28.7 - - - -
2L LEU 3.9 15.5 - - - +
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Residues in contact with LEU 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I THR* 3.9 10.3 - - + -
346I THR* 3.8 17.7 - - + -
354K ASP 2.9 18.6 + - - +
357K MET* 1.3 82.1 - - + +
359K SER* 1.3 64.2 + - - +
360K ASP 3.3 0.5 + - - -
361K ARG* 3.6 12.6 + - + +
362K TYR* 3.9 11.6 - - + -
2L LEU* 3.7 25.1 - - + +
3L ASP* 3.7 45.5 - - - +
4L PHE* 3.4 37.3 - - + +
13L LEU* 5.7 0.3 - - - +
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Residues in contact with SER 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I ALA* 3.7 14.6 - - - +
339I LEU* 4.6 1.8 - - - -
342I THR* 3.4 20.3 + - - -
301K ASN* 3.0 26.1 + - - -
355K LEU 3.1 12.2 + - - -
356K MET* 3.3 15.3 - - - -
358K LEU* 1.3 76.4 - - - +
360K ASP* 1.3 72.4 + - - +
363K ARG* 3.4 11.4 + - - -
4L PHE* 5.0 0.9 - - - -
12L VAL* 4.6 5.3 - - - +
13L LEU* 3.6 13.2 - - - +
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Residues in contact with ASP 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335I TYR* 3.2 9.7 - - - -
298K VAL 4.1 4.5 - - - +
299K MET* 3.3 15.7 - - - -
301K ASN* 2.7 33.1 + - - -
302K LEU* 2.9 24.7 + - + -
356K MET 3.9 0.2 + - - -
357K MET 3.2 3.8 + - - -
359K SER* 1.3 91.2 + - - +
361K ARG* 1.3 66.9 + - - +
362K TYR 2.9 4.5 + - - -
363K ARG* 2.7 43.0 + - - +
367K ALA* 3.1 15.2 - - + +
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Residues in contact with ARG 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302K LEU* 4.0 9.2 - - + -
357K MET* 2.9 34.4 + - - +
358K LEU* 3.6 9.3 + - - +
360K ASP* 1.3 77.7 - - - +
362K TYR* 1.3 94.0 + - + +
364K ASP 4.1 0.5 - - - +
368K TYR* 3.2 66.4 + - + +
371K ALA* 3.7 9.6 - - + +
373K ASP* 2.5 46.5 + - - -
374K ASN* 3.7 9.5 + - - +
1L MET* 3.9 12.0 - - - -
2L LEU 5.6 0.6 + - - -
3L ASP* 4.7 2.7 - - - -
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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