Contacts of the helix formed by residues 356 - 373 (chain A) in PDB entry 4IVR
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 GLY 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A THR* 3.3 4.2 - - - -
355A PRO* 1.3 78.5 - - - +
357A SER* 1.3 57.6 + - - +
358A ILE 3.2 2.7 - - - -
359A PRO* 3.2 19.4 - - - +
360A THR* 2.4 29.8 + - - -
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Residues in contact with SER 357 (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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142A HIS* 3.3 28.8 + - - +
352A VAL* 3.6 20.4 - - - -
353A THR* 3.7 5.4 + - - -
354A THR* 2.8 41.3 + - - -
355A PRO 3.2 1.2 - - - -
356A GLY* 1.3 78.0 - - - +
358A ILE* 1.3 53.0 + - - +
360A THR* 3.2 2.9 + - - -
361A ILE* 2.7 41.9 + - - +
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 4.2 25.1 - - + -
48A THR 4.2 13.7 - - - +
49A LEU* 4.9 2.2 - - + -
156A ALA* 4.4 10.8 - - + +
157A LEU* 3.7 36.7 - - + +
352A VAL* 3.7 29.6 - - + -
355A PRO 4.3 4.9 - - - +
357A SER* 1.3 76.1 - - - +
359A PRO* 1.3 65.3 - - + +
361A ILE* 3.3 4.0 + - + +
362A CYS* 2.9 31.6 + - - +
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Residues in contact with PRO 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PRO 4.1 2.5 - - - +
356A GLY* 3.2 24.7 - - - +
358A ILE* 1.3 97.6 - - + +
360A THR* 1.3 57.7 + - - +
362A CYS* 3.3 9.5 + - + +
363A ASP* 2.9 28.1 + - - +
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A HIS* 4.0 25.3 - - + +
356A GLY 2.4 23.7 + - - -
357A SER* 3.2 6.9 + - - -
358A ILE 3.2 0.2 - - - -
359A PRO* 1.3 77.6 - - - +
361A ILE* 1.3 65.0 + - - +
363A ASP* 3.2 8.1 + - + +
364A LEU* 3.2 22.2 + - + +
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Residues in contact with ILE 361 (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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49A LEU* 3.9 27.8 - - + -
139A LEU* 4.6 13.4 - - + +
142A HIS* 4.0 33.4 - - + -
143A ILE* 4.8 2.9 - - + -
157A LEU* 4.0 14.6 - - + -
159A LEU* 3.7 30.1 - - + -
352A VAL* 4.3 9.4 - - + -
357A SER 2.7 29.0 + - - +
358A ILE* 3.6 5.2 - - - +
360A THR* 1.3 71.6 - - - +
362A CYS* 1.3 62.6 + - - +
364A LEU* 3.3 7.9 + - - +
365A ALA* 3.1 21.5 + - + +
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Residues in contact with CYS 362 (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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76A ASP* 5.5 6.7 - - - -
79A VAL* 4.0 14.8 - - - -
157A LEU* 3.5 35.7 - - - -
358A ILE* 2.9 15.7 + - - +
359A PRO* 3.4 13.7 - - + +
361A ILE* 1.3 77.7 - - - +
363A ASP* 1.3 63.0 + - - +
365A ALA* 3.4 2.6 + - - +
366A ARG* 3.0 49.5 + - - +
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Residues in contact with ASP 363 (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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359A PRO 2.9 14.3 + - - +
360A THR* 3.2 9.5 + - + +
362A CYS* 1.3 74.8 - - - +
364A LEU* 1.3 53.8 + - - +
366A ARG* 3.2 7.9 + - - +
367A THR* 2.6 55.5 + - - -
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Residues in contact with LEU 364 (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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138A VAL* 5.5 6.5 - - + -
139A LEU* 4.7 15.7 - - + -
360A THR* 3.2 10.6 + - + +
361A ILE* 3.7 10.3 - - - +
362A CYS 3.3 0.2 - - - -
363A ASP* 1.3 84.0 + - - +
365A ALA* 1.3 57.2 + - - +
367A THR* 3.4 5.7 + - - -
368A PHE* 2.9 31.1 + - - +
310B TRP* 4.0 18.1 - - + +
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Residues in contact with ALA 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.6 28.9 - - + -
80A TYR 3.9 4.8 - - - +
81A VAL* 4.0 26.2 - - + -
159A LEU* 4.3 9.0 - - + -
361A ILE 3.1 13.5 + - - +
362A CYS* 3.9 2.0 - - - +
364A LEU* 1.3 78.0 - - - +
366A ARG* 1.3 62.7 + - - +
368A PHE* 3.4 4.6 + - - +
369A ALA* 3.1 23.9 + - - +
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Residues in contact with ARG 366 (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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75A ARG* 3.4 24.9 + - - +
76A ASP* 3.8 19.0 - - - +
79A VAL* 4.0 21.1 - - + +
362A CYS* 3.0 39.5 + - - +
363A ASP* 3.7 6.5 - - - +
365A ALA* 1.3 73.9 - - - +
367A THR* 1.3 66.0 + - - +
369A ALA* 3.4 5.7 + - - +
370A ARG* 3.2 48.8 + - - +
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Residues in contact with THR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASP* 2.6 45.5 + - - -
364A LEU* 3.5 5.8 - - - -
366A ARG* 1.3 75.6 - - - +
368A PHE* 1.3 61.4 + - - +
370A ARG* 3.5 16.4 + - - +
371A GLU* 3.3 20.3 + - - +
306B ASN* 3.4 37.6 + - - +
310B TRP* 3.5 17.5 - - + -
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Residues in contact with PHE 368 (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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81A VAL* 3.7 23.3 - - + -
82A PRO* 3.4 30.1 - - + -
84A PRO* 4.2 5.4 - - + -
131A PRO* 3.8 26.0 - - + -
132A TYR* 5.8 3.4 - + - -
134A VAL* 5.4 0.2 - - + -
135A THR* 3.3 27.1 - - + -
364A LEU 2.9 18.1 + - - +
365A ALA* 3.5 7.9 - - - +
367A THR* 1.3 76.3 - - - +
369A ALA* 1.3 57.8 + - - +
371A GLU* 3.1 3.4 + - - +
372A MET* 2.9 68.0 + - + +
307B VAL* 5.2 0.4 - - + -
310B TRP* 3.6 22.4 - + + -
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 6.2 0.4 - - + -
80A TYR* 4.0 7.6 - - + +
82A PRO* 3.6 30.7 - - + -
365A ALA 3.1 14.9 + - - +
366A ARG* 3.9 5.8 - - - +
368A PHE* 1.3 72.0 - - - +
370A ARG* 1.3 67.4 + - - +
373A GLY* 3.1 24.3 + - - +
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Residues in contact with ARG 370 (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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366A ARG* 3.2 43.8 + - - +
367A THR* 3.6 19.2 + - - +
369A ALA* 1.3 79.2 - - - +
371A GLU* 1.3 60.2 + - + +
373A GLY 5.0 2.4 - - - +
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Residues in contact with GLU 371 (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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86A THR* 3.6 19.4 + - - +
91A LEU* 4.6 3.3 - - + +
367A THR 3.3 13.1 + - - +
368A PHE* 3.1 5.3 + - - +
370A ARG* 1.3 82.0 - - + +
372A MET* 1.3 69.4 + - + +
373A GLY 4.9 0.9 - - - -
305B TYR* 3.4 30.4 - - + +
306B ASN* 2.8 52.7 + - + +
307B VAL* 3.0 21.5 + - - +
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Residues in contact with MET 372 (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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82A PRO* 5.0 0.2 - - - -
83A GLU 3.3 3.1 - - - +
84A PRO* 3.3 36.3 - - + +
86A THR* 3.3 19.2 + - - -
87A TYR* 4.1 21.5 - - + +
91A LEU* 4.8 4.5 - - + -
131A PRO* 4.3 1.6 - - - -
368A PHE* 2.9 59.0 + - + +
371A GLU* 1.3 94.3 - - + +
373A GLY* 1.3 66.1 + - - +
307B VAL* 3.5 38.6 - - + -
310B TRP* 3.9 7.4 - - + -
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 3.7 19.4 - - - +
83A GLU 3.5 11.0 - - - -
86A THR* 3.9 5.5 + - - -
369A ALA 3.1 19.1 + - - +
370A ARG 5.0 1.9 - - - +
371A GLU 4.9 1.0 - - - -
372A MET* 1.3 81.3 + - - +
374A GLU* 1.3 66.2 + - - +
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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