Contacts of the helix formed by residues 348 - 364 (chain C) in PDB entry 2VGB
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 348 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 2.9 45.4 + - + +
80A SER 3.9 8.9 + - - -
81A GLU* 3.3 25.8 + - - -
427A GLU* 3.0 41.1 + - - +
344C ILE* 3.9 14.1 - - + -
345C PRO* 2.9 36.0 + - + +
347C GLU* 1.3 82.8 - - + +
349C VAL* 1.3 66.5 + - - +
350C PHE 3.3 2.7 - - - -
351C LEU* 3.0 27.2 + - + +
352C ALA 3.3 3.5 + - - -
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG* 4.9 8.5 - - + -
388A THR* 4.9 5.4 - - + -
335C VAL* 5.2 0.2 - - + -
337C ARG* 3.8 33.4 - - + +
340C LEU* 4.2 16.6 - - + +
341C GLY* 3.6 33.2 - - - +
344C ILE* 3.9 9.4 - - + +
345C PRO 3.8 5.8 + - - +
346C ALA* 3.6 15.1 + - - +
348C LYS* 1.3 74.5 - - - +
350C PHE* 1.3 58.7 + - - +
352C ALA* 2.6 26.2 + - - +
353C GLN* 2.8 15.9 + - + +
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Residues in contact with PHE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU* 5.6 0.4 - - + -
388A THR* 4.6 7.4 - - + +
389A SER* 4.5 20.4 - - - -
392A ALA* 3.5 32.3 - - + -
396A LEU* 4.3 9.9 - - + -
424A ILE* 4.5 6.7 - - + -
427A GLU* 3.6 12.1 - - + -
428A ALA* 3.6 30.3 - - - -
431A ALA* 4.5 3.8 - - + -
347C GLU 3.2 28.5 - - - -
348C LYS 3.3 0.2 - - - -
349C VAL* 1.3 78.9 - - - +
351C LEU* 1.3 87.0 + - + +
353C GLN* 3.7 10.1 - - - +
354C LYS* 2.8 56.0 + - + +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 3.9 23.6 - - - +
76A LEU* 4.2 25.4 - - + +
78A ILE* 3.9 15.9 - - + +
427A GLU* 3.6 25.8 - - - +
431A ALA* 4.0 16.8 - - + -
348C LYS* 3.0 31.0 + - + +
350C PHE* 1.3 107.8 - - + +
352C ALA* 1.3 64.6 + - - +
354C LYS* 4.1 0.2 - - - -
355C MET* 3.1 25.8 + - - +
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Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.8 17.0 - - + +
320C VAL* 4.2 13.2 - - + -
340C LEU* 3.9 16.4 - - + -
344C ILE* 4.7 2.0 - - + -
348C LYS 3.3 3.1 + - - +
349C VAL* 2.6 15.0 + - - +
351C LEU* 1.3 74.5 - - - +
353C GLN* 1.3 61.7 + - - +
355C MET* 3.3 8.7 + - - +
356C MET* 2.9 47.4 + - + +
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Residues in contact with GLN 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A SER* 5.2 7.0 + - - -
393A ASN* 6.1 0.8 - - - +
335C VAL* 3.8 25.1 - - + +
337C ARG* 3.0 36.0 + - - +
349C VAL* 2.8 18.0 + - + +
350C PHE* 3.7 13.0 - - - +
352C ALA* 1.3 74.3 - - - +
354C LYS* 1.3 64.8 + - - +
356C MET* 3.4 0.9 + - - +
357C ILE* 3.0 38.2 + - + +
369C CYS* 3.7 19.0 - - - -
390C ASP* 5.2 1.6 + - - -
393C ASN* 4.9 0.8 - - - +
394C ALA* 4.0 11.7 - - - +
397C ASP* 2.9 26.7 + - - +
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Residues in contact with LYS 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.1 26.0 - - + +
76A LEU* 4.3 18.6 - - + -
389A SER* 6.3 0.2 - - - -
392A ALA* 5.5 0.2 - - - -
393A ASN* 2.8 32.9 + - - +
396A LEU* 4.0 21.0 - - + +
350C PHE* 2.8 43.1 + - + +
353C GLN* 1.3 76.3 - - + +
355C MET* 1.3 57.0 + - - +
357C ILE* 4.0 4.1 - - - +
358C GLY* 3.0 25.8 + - - -
393C ASN* 5.3 0.4 + - - +
397C ASP* 2.8 45.2 + - - +
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Residues in contact with MET 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU 3.5 15.1 + - - +
74A CYS* 3.8 7.8 - - - +
76A LEU* 3.7 21.5 - - + +
78A ILE* 6.4 0.2 - - + -
320C VAL* 4.0 33.7 - - + +
323C PHE* 4.5 5.2 - - + -
351C LEU 3.1 18.8 + - - +
352C ALA* 3.6 4.7 - - - +
354C LYS* 1.3 75.5 - - - +
356C MET* 1.3 79.7 + - + +
358C GLY* 3.4 1.2 + - - -
359C ARG* 3.0 69.1 + - - +
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Residues in contact with MET 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 3.7 34.1 - - + -
320C VAL* 4.5 3.6 - - + -
323C PHE* 3.4 42.3 - - + -
333C ILE* 4.4 6.7 - - + -
335C VAL* 3.8 34.1 - - + -
340C LEU* 4.0 6.1 - - + -
352C ALA* 2.9 38.1 + - + +
353C GLN 4.1 1.6 - - - +
355C MET* 1.3 88.0 - - + +
357C ILE* 1.3 57.0 + - - +
359C ARG* 3.0 2.3 + - - +
360C CYS* 2.8 40.2 + - - -
367C VAL* 4.8 0.7 - - + -
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Residues in contact with ILE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C VAL* 4.5 4.7 - - + -
353C GLN* 3.0 35.3 + - + +
354C LYS 4.0 2.5 - - - +
356C MET* 1.3 73.8 - - - +
358C GLY* 1.3 64.2 + - - +
360C CYS* 3.5 0.5 + - - +
361C ASN* 2.9 25.6 + - - +
367C VAL* 4.0 24.2 - - + -
369C CYS* 4.8 7.2 - - + -
394C ALA 4.2 0.9 - - - +
397C ASP* 3.4 45.5 - - + +
398C GLY* 3.4 21.5 - - - +
399C ALA* 3.8 23.6 - - + -
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Residues in contact with GLY 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.9 16.3 - - - +
73A LEU* 4.7 11.0 - - - -
74A CYS* 3.7 14.8 - - - -
354C LYS 3.0 18.4 + - - -
355C MET 3.8 1.3 - - - -
357C ILE* 1.3 78.9 - - - +
359C ARG* 1.3 55.6 + - - +
361C ASN* 3.2 6.2 + - - +
362C LEU* 3.0 25.6 + - - +
397C ASP 5.3 0.9 + - - -
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Residues in contact with ARG 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A CYS* 2.7 52.1 + - + -
75A LEU* 4.9 4.6 - - - +
76A LEU 5.2 1.0 + - - -
320C VAL 5.3 1.6 + - - -
321C LYS 5.8 2.0 + - - -
323C PHE* 3.6 27.1 - - + +
324C ASP* 3.1 41.4 + - - +
327C LEU* 4.2 5.6 - - + +
355C MET* 3.0 48.0 + - - +
356C MET 3.0 0.4 + - - +
358C GLY* 1.3 73.4 - - - +
360C CYS* 1.3 60.0 + - - +
362C LEU* 3.1 11.7 + - + +
363C ALA* 2.8 27.7 + - - +
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Residues in contact with CYS 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C PHE* 4.0 7.9 - - - -
327C LEU* 4.3 14.1 - - - -
333C ILE* 3.7 37.2 - - - -
356C MET 2.8 22.3 + - - +
357C ILE 3.9 1.3 - - - +
359C ARG* 1.3 69.1 - - - +
361C ASN* 1.3 69.0 + - - +
363C ALA* 2.7 14.1 + - - +
364C GLY 2.7 11.4 + - - -
365C LYS 3.3 23.1 + - - +
366C PRO 4.2 4.3 - - - -
367C VAL* 3.7 22.2 - - + -
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Residues in contact with ASN 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.6 7.5 - - + +
357C ILE* 2.9 19.0 + - - +
358C GLY* 3.3 11.6 - - - +
360C CYS* 1.3 75.4 - - - +
362C LEU* 1.3 63.3 + - - +
364C GLY* 3.2 11.0 + - - -
365C LYS 5.2 0.9 + - - -
367C VAL* 4.4 5.1 - - - +
397C ASP 3.8 5.4 - - - +
398C GLY* 2.8 40.7 + - - +
400C ASP* 4.7 0.6 + - - -
437C LEU* 4.9 13.1 - - + +
441C LEU* 3.9 20.7 - - + +
486C ARG* 3.8 11.4 + - - +
488C ARG* 3.2 25.8 + - - +
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Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.4 32.1 - - + -
71A GLU* 5.8 1.8 - - - +
74A CYS* 4.4 13.2 - - - -
358C GLY 3.0 10.8 + - - +
359C ARG* 3.1 15.5 - - + +
360C CYS 3.0 0.2 - - - -
361C ASN* 1.3 76.4 - - - +
363C ALA* 1.3 57.9 + - - +
364C GLY 3.1 0.2 - - - -
441C LEU* 4.6 4.2 - - + +
444C ALA* 3.9 24.5 - - + +
445C ALA* 5.7 2.0 - - - +
486C ARG* 2.8 28.4 + - - +
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Residues in contact with ALA 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C LEU* 3.5 31.6 - - + -
359C ARG 2.8 6.6 + - - +
360C CYS 2.7 8.6 + - - +
362C LEU* 1.3 73.5 - - - +
364C GLY* 1.3 61.6 + - - +
365C LYS* 3.4 18.4 - - + +
486C ARG* 3.9 8.4 + - - -
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Residues in contact with GLY 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C CYS 2.7 8.0 + - - -
361C ASN* 3.2 6.7 + - - -
362C LEU 3.1 4.8 - - - -
363C ALA* 1.3 80.5 - - - +
365C LYS* 1.3 57.9 + - - +
482C GLN* 3.1 23.0 + - - +
486C ARG* 3.5 35.3 - - - +
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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
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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