Contacts of the helix formed by residues 349 - 361 (chain A) in PDB entry 4G3D
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 GLN 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A GLY* 1.3 83.5 - - - +
350A ALA* 1.3 66.2 + - - +
351A HIS* 3.4 20.6 + - + +
352A SER* 3.6 12.2 + - - +
353A LEU 3.5 11.3 + - - -
380A VAL* 3.6 3.5 - - - +
382A LEU* 3.4 12.7 - - - +
559B THR* 5.7 2.2 - - + -
561B THR* 4.2 9.3 - - + +
593B CYS* 6.0 0.6 - - - +
594B HIS* 3.5 49.5 + - + +
597B THR* 3.8 18.2 + - - +
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Residues in contact with ALA 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 1.3 73.7 - - - +
351A HIS* 1.3 63.1 + - + +
353A LEU* 3.0 6.5 + - - +
354A THR* 2.8 32.8 + - - -
382A LEU* 3.7 15.0 - - + +
445A ALA* 3.7 25.0 - - + +
446A GLY* 4.0 16.2 - - - +
601B ARG* 3.9 14.8 - - + -
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Residues in contact with HIS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLN* 3.7 23.2 + - + +
350A ALA* 1.3 75.5 + - + +
352A SER* 1.3 57.3 + - - +
354A THR* 3.5 2.8 + - - -
355A SER* 2.9 34.5 + - - -
560B GLU* 3.2 19.7 - - + +
561B THR* 3.6 13.6 - - + +
597B THR* 4.3 19.9 + - - +
600B PHE 4.3 5.8 - - - -
601B ARG* 3.7 30.7 - - + +
602B GLY 3.7 19.4 + - - +
604B LEU* 3.5 45.1 - - + +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 5.4 0.9 - - - +
341A LEU* 3.7 34.5 - - - +
348A GLY* 5.3 1.5 - - - -
349A GLN* 3.6 20.2 + - - +
350A ALA 3.2 0.4 - - - -
351A HIS* 1.3 77.2 - - - +
353A LEU* 1.3 58.2 + - - +
355A SER* 3.2 3.5 + - - -
356A LEU* 2.8 31.4 + - - +
380A VAL* 4.0 11.7 - - - -
560B GLU* 3.9 15.5 + - - +
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Residues in contact with LEU 353 (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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349A GLN 3.5 4.9 + - - +
350A ALA* 3.0 13.1 + - - +
352A SER* 1.3 79.5 - - - +
354A THR* 1.3 52.2 + - - +
356A LEU* 3.3 2.4 + - + +
357A ALA* 2.7 36.1 + - - +
360A TRP* 4.2 12.3 - - + -
380A VAL* 3.8 28.4 - - + +
382A LEU* 4.1 10.3 - - + -
441A LEU* 4.5 9.2 - - + -
445A ALA* 5.2 2.0 - - + -
455A LEU* 4.0 21.1 - - + -
457A GLY* 3.9 9.2 - - - -
458A ALA* 3.6 52.7 - - + +
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Residues in contact with THR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA 2.8 20.5 + - - -
351A HIS* 3.6 6.5 - - - -
353A LEU* 1.3 69.6 - - - +
355A SER* 1.3 66.0 + - - +
357A ALA* 3.1 17.6 + - - +
358A LYS* 3.1 30.9 + - - +
438A ALA* 4.8 0.3 - - - +
441A LEU* 4.8 4.2 + - - +
442A MET* 3.8 24.3 - - + -
445A ALA* 4.2 7.8 - - - +
601B ARG* 3.4 37.7 + - - +
602B GLY* 4.7 7.6 - - - +
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 2.9 34.2 + - - +
337A LEU* 4.5 10.3 - - - +
338A VAL* 3.7 24.7 - - - +
341A LEU* 4.8 0.9 - - - -
351A HIS 2.9 19.1 + - - -
352A SER* 3.6 5.8 - - - -
354A THR* 1.3 74.1 - - - +
356A LEU* 1.3 64.2 + - - +
358A LYS* 3.1 22.4 + - - +
359A THR 3.5 2.8 + - - -
560B GLU* 4.6 2.8 + - - -
602B GLY 4.3 7.3 + - - -
603B PRO* 5.2 0.2 - - - +
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Residues in contact with LEU 356 (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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338A VAL* 4.1 6.4 - - + +
341A LEU* 4.4 23.8 - - + +
342A GLN* 3.9 28.7 - - + -
352A SER 2.8 16.8 + - - +
353A LEU* 3.5 5.6 - - + +
355A SER* 1.3 75.3 - - - +
357A ALA* 1.3 63.7 + - - +
359A THR* 2.9 28.7 + - - +
360A TRP* 3.3 31.0 + - + +
378A GLU* 4.4 6.5 - - + +
379A GLY* 3.6 39.0 - - - +
380A VAL* 4.2 8.5 - - + -
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Residues in contact with ALA 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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353A LEU 2.7 17.7 + - - +
354A THR* 3.2 17.0 - - - +
356A LEU* 1.3 73.5 - - - +
358A LYS* 1.3 54.0 - - - +
360A TRP* 2.9 32.6 + - + +
361A ALA 3.1 9.4 + - - -
436A PHE* 3.4 7.2 - - + -
438A ALA* 3.8 20.2 - - + +
441A LEU* 4.1 25.1 - - + -
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Residues in contact with LYS 358 (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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334A GLU* 3.5 31.1 + - - +
354A THR* 3.1 30.7 + - - +
355A SER 3.1 7.7 + - - +
357A ALA* 1.3 75.0 - - - +
359A THR* 1.3 63.9 + - - +
361A ALA* 3.2 20.3 + - - +
362A ALA* 3.7 6.6 + - - +
438A ALA* 4.0 15.3 - - + -
442A MET* 3.9 26.0 - - - +
602B GLY* 5.9 2.8 - - - -
603B PRO* 5.6 8.2 - - - +
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Residues in contact with THR 359 (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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338A VAL* 4.1 20.4 - - - +
342A GLN* 3.3 31.8 + - - +
355A SER 3.5 2.8 + - - -
356A LEU* 2.9 18.8 + - + +
358A LYS* 1.3 78.4 - - - +
360A TRP* 1.3 73.8 + - + +
362A ALA* 3.1 22.9 + - - +
378A GLU* 4.5 5.6 - - - +
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Residues in contact with TRP 360 (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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353A LEU* 4.2 11.7 - - + -
356A LEU* 3.3 30.0 + - + +
357A ALA* 2.9 16.1 + - - +
359A THR* 1.3 81.9 - - + +
361A ALA* 1.3 56.8 + - - +
362A ALA 3.0 10.6 + - - +
378A GLU* 2.9 47.5 + - - -
379A GLY* 4.2 1.8 - - - -
433A LEU* 3.4 31.9 - - + +
436A PHE* 3.7 28.9 - + + -
441A LEU* 4.4 4.0 - - + -
458A ALA* 3.5 35.7 - - + -
460A ARG* 3.5 32.4 - - + +
465A VAL* 3.9 23.1 - - + -
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Residues in contact with ALA 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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357A ALA 3.1 11.1 + - - +
358A LYS* 3.2 11.3 + - - +
360A TRP* 1.3 74.1 - - - +
362A ALA* 1.3 60.6 + - - +
433A LEU 5.5 0.4 - - - -
436A PHE* 3.8 23.8 - - + +
437A ARG* 4.4 1.3 - - - -
438A ALA* 3.9 20.2 - - + +
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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