Contacts of the helix formed by residues 339 - 353 (chain C) in PDB entry 3G1Q
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 MET 339 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 4.7 1.3 - - + -
322C GLU* 3.4 9.6 - - + +
323C ILE* 4.0 12.1 - - + -
326C PHE* 3.6 25.6 - - + -
334C ASN 3.5 10.3 - - - +
335C VAL* 3.5 39.0 + - - +
336C MET 5.1 0.4 + - - -
337C ASP 3.5 1.4 - - - -
338C GLU* 1.3 77.6 - - - +
340C PRO* 1.4 63.4 - - - +
341C PHE 3.2 2.7 - - - -
342C ALA* 3.3 29.7 + - + -
343C GLU* 3.1 17.3 + - - +
433C LYS* 3.4 39.5 + - + +
437C ALA* 3.7 21.8 - - + +
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Residues in contact with PRO 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C GLU* 3.4 9.4 - - - +
337C ASP 4.3 5.8 - - - +
338C GLU* 3.2 11.4 - - - +
339C MET* 1.4 89.5 - - - +
341C PHE* 1.3 61.7 + - + +
343C GLU* 3.7 8.0 + - + +
344C ARG* 3.1 28.1 + - - +
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C HIS* 3.3 46.0 - - - -
318C ALA* 3.8 15.7 - - + +
319C LEU* 3.9 20.6 - - + -
322C GLU* 2.7 28.2 + - + +
340C PRO* 1.3 74.8 - - + +
342C ALA* 1.3 58.2 + - - +
344C ARG* 3.0 16.3 + - - +
345C CYS* 2.9 49.6 + - - -
402C PRO* 4.0 17.5 - - + -
403C GLU* 4.0 23.1 - - + -
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Residues in contact with ALA 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU* 3.8 17.5 - - + -
322C GLU* 2.9 12.3 + - - +
339C MET* 3.3 35.8 + - + +
341C PHE* 1.3 75.4 - - - +
343C GLU* 1.3 62.3 + - - +
345C CYS* 3.2 9.5 + - - +
346C ALA* 3.0 22.7 + - - +
433C LYS* 4.1 10.3 - - + -
436C LEU* 4.2 12.2 - - + +
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C MET* 5.3 2.8 - - - +
339C MET 3.1 15.5 + - - +
340C PRO* 3.7 9.1 - - + +
342C ALA* 1.3 77.5 - - - +
344C ARG* 1.3 56.5 + - + +
346C ALA* 3.2 5.1 + - - +
347C ARG* 2.8 56.6 + - + +
425C GLN* 5.3 1.2 - - - +
429C LEU* 4.2 23.4 - - + +
433C LYS* 3.1 32.2 + - + +
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Residues in contact with ARG 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PRO* 3.1 18.8 + - - +
341C PHE* 3.0 21.3 + - - +
343C GLU* 1.3 74.1 - - + +
345C CYS* 1.3 67.0 + - - +
347C ARG* 3.9 9.3 - - - +
348C GLU* 2.9 27.9 + - - +
402C PRO* 2.8 44.6 + - + +
403C GLU* 3.4 14.0 + - - +
404C ARG 3.0 21.6 + - - -
405C ASP* 2.8 23.8 + - - -
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Residues in contact with CYS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C SER* 4.1 4.0 - - - -
307C LEU* 4.1 20.6 - - + -
319C LEU* 5.5 0.7 - - - -
341C PHE* 2.9 47.1 + - - -
342C ALA* 3.2 11.6 + - - +
344C ARG* 1.3 78.8 - - - +
346C ALA* 1.3 57.4 + - - +
348C GLU 3.3 0.2 + - - -
349C SER* 2.9 32.1 + - - -
400C TRP* 3.6 34.8 + - + -
402C PRO* 3.9 4.9 - - - -
436C LEU* 4.8 4.7 - - + -
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Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 3.8 6.3 - - + +
303C SER* 3.4 12.8 - - - -
342C ALA 3.0 12.8 + - - +
343C GLU* 3.7 4.9 - - - +
345C CYS* 1.3 76.0 - - - +
347C ARG* 1.3 63.7 + - - +
349C SER* 3.2 4.5 + - - -
350C ILE* 3.1 27.5 + - - +
429C LEU* 3.7 26.2 - - + -
432C VAL* 3.8 24.0 - - + -
433C LYS* 5.2 1.8 - - + -
436C LEU* 5.2 0.2 - - + -
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Residues in contact with ARG 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASN* 3.1 37.0 + - - +
337A ASP* 5.7 1.0 + - - -
338A GLU* 5.3 4.4 + - - -
343C GLU* 2.8 44.7 + - + +
344C ARG* 3.9 8.7 - - - +
346C ALA* 1.3 76.7 - - - +
348C GLU* 1.3 56.6 + - - +
350C ILE* 3.3 10.3 + - - +
351C ARG* 2.9 28.4 + - - +
412C PHE* 3.7 45.1 - - + +
415C PHE* 4.5 12.7 - - + -
425C GLN* 3.9 20.4 + - - -
429C LEU* 4.9 5.6 - - + +
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Residues in contact with GLU 348 (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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344C ARG 2.9 19.0 + - - +
345C CYS 3.8 0.2 - - - +
347C ARG* 1.3 72.6 - - - +
349C SER* 1.3 61.0 + - - +
351C ARG* 2.7 44.1 + - - +
352C ARG* 2.9 29.6 + - - +
399C ARG 3.3 1.4 - - - +
400C TRP* 3.4 17.2 - - + +
401C ASP 2.9 38.1 + - - +
402C PRO* 3.8 10.1 - - + -
404C ARG* 2.9 29.6 - - + +
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Residues in contact with SER 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 4.3 5.6 - - - -
302C TRP* 3.8 21.7 - - - -
303C SER* 3.2 28.1 + - - -
306C HIS* 3.6 4.3 - - - -
345C CYS 2.9 11.3 + - - -
346C ALA 3.2 8.9 + - - -
348C GLU* 1.3 77.6 - - - +
350C ILE* 1.3 56.1 + - - +
352C ARG* 4.1 1.4 - - - +
353C ASP* 3.0 32.9 + - - +
400C TRP* 3.1 21.5 + - - +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 3.5 32.5 - - + +
346C ALA 3.1 15.1 + - - +
347C ARG* 3.6 7.6 - - - +
349C SER* 1.3 72.5 - - - +
351C ARG* 1.3 68.1 + - - +
353C ASP 4.2 6.5 - - - -
354C PRO* 2.9 28.2 - - + +
355C PRO* 4.1 14.8 - - + -
388C HIS* 3.5 0.5 - - - -
412C PHE* 4.0 5.8 - - + -
414C GLY* 3.6 35.2 - - - +
415C PHE* 3.4 35.9 - - + -
429C LEU* 5.0 2.2 - - + -
480C HEM 4.0 7.6 - - + -
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Residues in contact with ARG 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG 2.9 17.0 + - - +
348C GLU* 2.7 47.0 + - - +
350C ILE* 1.3 77.7 - - - +
352C ARG* 1.3 79.4 + - - +
354C PRO* 3.5 1.2 - - - +
388C HIS* 2.8 70.1 + - + +
389C HIS* 4.1 3.4 - - - -
394C PHE* 3.9 27.6 - - + +
397C PRO* 2.6 42.9 + - - +
399C ARG 3.2 9.7 + - - -
404C ARG* 3.5 15.9 - - - +
412C PHE* 3.9 15.9 - - + -
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Residues in contact with ARG 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C TRP* 4.0 4.8 - - - -
306C HIS* 3.7 30.1 - - - -
348C GLU 2.9 18.9 + - - +
349C SER 4.1 1.8 - - - +
351C ARG* 1.3 94.2 - - - +
353C ASP* 1.3 91.7 + - - +
354C PRO* 3.6 1.2 - - - +
385C LEU* 4.9 0.9 - - - +
389C HIS* 3.2 11.3 + - - -
397C PRO 3.9 10.3 - - - +
398C ARG* 2.9 83.1 + - - +
400C TRP* 3.9 15.7 - - + +
452C VAL* 3.9 21.2 - - - +
453C PRO 4.8 0.8 + - - -
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Residues in contact with ASP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C TRP* 3.5 43.7 + - + +
306C HIS* 4.3 1.7 + - - -
349C SER 3.0 15.1 + - - +
350C ILE* 3.4 2.8 - - - -
352C ARG* 1.3 117.5 + - - +
354C PRO* 1.3 69.3 - - - +
355C PRO* 3.2 9.0 - - - +
385C LEU* 5.7 1.3 - - - +
398C ARG* 3.1 22.5 + - - -
455C PRO* 3.8 16.7 - - + +
457C TYR* 4.8 1.6 + - - -
462C VAL* 4.8 4.8 - - + +
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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